diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 0000000..788467f --- /dev/null +++ b/.github/workflows/deploy.yml @@ -0,0 +1,49 @@ +name: Deploy +on: + push: + branches: + - main + +jobs: + deploy: + runs-on: ubuntu-latest + permissions: + contents: write # To push a branch + pull-requests: write # To create a PR from that branch + steps: + - uses: actions/checkout@v3 + with: + fetch-depth: 0 + - name: Create executable directory + run: | + mkdir mdbook + echo `pwd`/mdbook >> $GITHUB_PATH + - name: Install mdbook + run: | + curl -sSL https://github.com/rust-lang/mdBook/releases/download/v0.4.36/mdbook-v0.4.36-x86_64-unknown-linux-gnu.tar.gz | tar -xz --directory=./mdbook + - name: Install mdbook-toc + run: | + curl -sSL https://github.com/badboy/mdbook-toc/releases/download/0.14.2/mdbook-toc-0.14.2-x86_64-unknown-linux-gnu.tar.gz | tar -xz --directory=./mdbook + - name: Install mdbook-mermaid + run: | + curl -sSL https://github.com/badboy/mdbook-mermaid/releases/download/v0.13.0/mdbook-mermaid-v0.13.0-x86_64-unknown-linux-gnu.tar.gz | tar -xz --directory=./mdbook + # curl -sSL https://raw.githubusercontent.com/badboy/mdbook-mermaid/main/src/bin/assets/mermaid-init.js -o mermaid-init.js + # curl -sSL https://raw.githubusercontent.com/badboy/mdbook-mermaid/main/src/bin/assets/mermaid.min.js -o mermaid.min.js + - name: Deploy GitHub Pages + run: | + # This assumes your book is in the root of your repository. + # Just add a `cd` here if you need to change to another directory. + mdbook-mermaid install . + mdbook build + git worktree add gh-pages + git config user.name "Deploy from CI" + git config user.email "" + cd gh-pages + # Delete the ref to avoid keeping history. + git update-ref -d refs/heads/gh-pages + rm -rf * + mv ../book/html/* . + ls + git add . + git commit -m "Deploy $GITHUB_SHA to gh-pages" + git push --force --set-upstream origin gh-pages diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..7585238 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +book diff --git a/23fs/fg/01_modern_genomics_i.html b/23fs/fg/01_modern_genomics_i.html new file mode 100644 index 0000000..12aba0a --- /dev/null +++ b/23fs/fg/01_modern_genomics_i.html @@ -0,0 +1,554 @@ + + + + + + Modern Genomics I - Notes @ ETH Zürich + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ +
+ + + + + + + + +
+
+

Modern Genomics I

+ +

Introduction

+

Molecular biology is governed by the "central dogma". Genomics is basically studying the DNA part of it.

+

Genome sequence: complete listing of all nucleotides of one organisms, in correct order, and mapped to the chromosomes.

+
graph LR
+    A[DNA] -->|Transcription| B[RNA]
+    B -->|Translation| C[Protein]
+
+

Timeline

+

Efficient sequencing technology arrived rather late. Initially the sequencing process was cumbersome and radioactive.

+
    +
  • 1975: "dideoxy" DNA sequencing (Sanger)
    • +
  • 1977: first genome (bacteriophage \( \phi X 174 \) )
    • +
  • 1995: first cell (Haemophilus influenzae)
    • +
  • 1998: first animal (Caenorhabditis elegans)
    • +
  • 2001: Homo sapiens
    • +
  • Today (February 2023) +
      +
    • genomes available for: 409,947 Bacteria, 4,988 Archaea, 47,200 Eukaryotes
      • +
    • human genomes fairly routine +
        +
      • below 1000$ raw costs
        • +
      • "Personal Genome Projects" are enrolling 100’000s of volunteers, including their medical records
        • +
      +
      • +
    +
    • +
+

Why Genomics?

+
    +
  • Because we want an inventory of all genes and functions
    • +
  • Because wea can compare genomes to learn about evolution, to get hints on gene function, etc +
      +
    • Comparison can be either based on DNA or protein
      • +
    • Alignments, dot plots, whole chromosome comparison
      • +
    +
    • +
+

Comparative genomics use case examples

+
    +
  • Gene prediction +
      +
    • Gene prediction algorithms that use homology (=comparative genomics result) information: SLAM, SGP, Twinscan (= N-SCAN)...
      • +
    • UCSC genome browser gene prediction
      • +
    +
    • +
  • Gene family evolution
    • +
+

Classical sequencing method

+

Sanger (double-deoxy) sequencing

+

Natural DNA extension requires 3'-OH. The dideoxy method uses a 2',3'-dideoxy nucleotide, which lacks the 3'-OH group. This causes the DNA chain to terminate. By introducing different dideoxy nucleotides, the sequence can be read.

+

Automated Dye Sequencing

+

Variants of Sanger sequencing. Still utilize the dideoxy method to terminate DNA elongation. The difference is that the dideoxy nucleotides are labeled with different fluorescent dyes. The sequence is read by a laser.

+

Two variants of Automated Dye Sequencing

+

Dye terminator sequencing is now widely used over the rather cumbersome (4 tubes per sample) dye primer chemistry.

+

New (Next-generation) sequencing technologies

+

Generally involves first amplifying the DNA, then sequencing it. Sequencing is done by detecting the nucleotides as they are incorporated into the growing DNA strand (sequencing by synthesis). High-throughput is achieved by parallelizing the sequencing process.

+

Amplification technologies

+

First-generation amplification technology: needs DNA-library in bacterial vectors --> cumbersome and biased

+

Improvement: get rid of bacteria

+

Emulsion PCR

+

Improvement: bacterium free, but still needs cloning

+
%%{init: {"graph": {"htmlLabels": false}} }%%
+graph TD
+    A["`**Fragment** the DNA, ligate **adapters** to ends, make **single-stranded**`"] --> B["Attach to microbeads"]
+    B --> C["`PCR-amplify, in a **water-oil emulsion**`"]
+    C --> D["`Enrich beads having successful amplifications, then place into regular lattice
+    (see figure below for details)`"]
+
+

Emulsion PCR enrichment step

+

In short, the enrichment is done by capturing the second (5'-end) primer of the PCR product onto a large polysyrene bead.

+

PCR on solid support

+

PCR on solid support

+

Barcoding and "linked reads"

+

Barcoding

+

10X technology

+

Sequencing technologies

+

First-generation sequencing needs DNA size-separation on a gel

+

Improvement: get rid of gel (sequencing by synthesis)

+

Pyrosequencing

+

Pyrosequencing

+

Reversible terminator sequencing

+

Reversible terminator sequencing

+

Sequencing by semi-conductor

+

Directly detects the release of H+ ions when a nucleotide is incorporated into the growing DNA strand.

+

Sequencing by semi-conductor

+

Current implementations of NGS

+
    +
  • Illumina +
      +
    • Illumina NovaSeq 6000
      • +
    • PCR on solid support
      • +
    • reversible terminator sequencing
      • +
    • read length ca. 250bp
      • +
    • 1e14 bp per run
      • +
    +
    • +
  • Ion Torrent / Life Techn. Inc +
      +
    • Ion Gene Studio S5
      • +
    • PCR on beads
      • +
    • sequencing by semi-conductor
      • +
    • read length ca. 600bp
      • +
    • 1e10 bp per run
      • +
    +
    • +
+

Third-generation sequencing technologies

+

Single molecule sequencing. No need for amplification.

+

Characterized by extremely long reads, but also high error rates.

+
    +
  • Pacific Biosciences +
      +
    • SMRT (single molecule real time) sequencing
      • +
    • pacbio1
      • +
    • pacbio1
      • +
    +
    • +
  • Oxford Nanopore +
      +
    • MinION
      • +
    • oxford nanopore
      • +
    +
    • +
+
+

Self-note: minimap2 is a popular aligner for long reads.

+
+

Environmental sequencing

+

Traditional genome sequencing requires individual cell isolation and cultivation. This is not possible for the majority of microorganisms. But one advantage is that it's possible to re-assemble the genome from the reads.

+

Environmental sequencing: directly sequence DNA extracted from the environment without purification and clonal cultivation. Genome assembly is generally not possible.

+
+

Self-note: data generated from environmental sequencing is typically large in size, but highly fragmented and contaminated. Lots of exciting research in this area.

+
+

How to deal with environmental sequencing data

+
    +
  • Novel gene discovery +
      +
    • Sequence identity comparison to known genes +
        +
      • But > 50% of the environmental genomes are not similar to any known genome
        • +
      +
      • +
    +
    • +
  • Novel gene families
    • +
  • Gene family clustering (similar samples have similar gene family distribution)
    • +
+

Single-cell sequencing

+

Why?

+
    +
  • Heterogeneity in cell populations +
      +
    • Tumor cells
      • +
    • Immune cells
      • +
    • Microbial communities
      • +
    • Developmental biology
      • +
    +
    • +
+

How?

+

In short, we first get single cells, then amplify the whole genome and sequence it.

+

The challenges lie in the bolded parts.

+

Single-cell isolation

+

(In the very first "single cell" genomics paper, the "single" cells were literally picked manually...nowadays we don't do that)

+
    +
  1. Sorting with optical tweezers +Optic tweezers
    2. +
  2. Dilution series
    3. +
  3. Flow sorting +Flow sorting
    4. +
+

Whole genome amplification

+

Steps summarized:

+
    +
  1. MDA
    2. +
  2. phi 29 debranching
    3. +
  3. S1 nuclease digestion
    4. +
  4. DNA pol I nick translation
    5. +
  5. Cloning
    6. +
+
    +
  • Isothermal Multiple displacement amplification (MDA) +
      +
    • Phi29 DNA polymerase
      • +
    • Random primers
      • +
    • Isothermal amplification
      • +
    +
    • +
+

MDA

+

After MDA, we obtained a "hyperbranched chromosome". After debranching and cloning, we can sequence and re-assemble the genome.

+

Next steps

+

The debranching is done by incubating phi 29 DNA pol with hyperbranched DNA without any primer. The strand-replacement activity of phi 29 DNA pol will remove the hyperbranched structure.

+

S1 nucleases are used to remove the remaining single-stranded DNA.

+

Nicks are filled in by DNA pol I (has 5'->3' exonuclease activity).

+

Genomic databases

+

This section likely won't be covered in the exam.

+
+

General popular resources:

+
    +
  • Raw data: NCBI sequence read archive (SRA) (also it's European counterpart, EBI European Nucleotide Archive (ENA), but they are basically the same thing now) +
      +
    • seq quality score included
      • +
    • but incomplete: legacy & newer data not available
      • +
    • gigantic in size
      • +
    +
    • +
  • Sequencing projects: GOLD (Genomes OnLine Database) +
      +
    • keep track of "who is sequencing what" and responsible researchers (contacts), funding sources, sequencing centers etc
      • +
    +
    • +
  • Genome browsers +
      +
    • Display features (genes, transcripts...) on the genomes, show annotations (conflicts, variants also included), homolog search
      • +
    • UCSC genome browser, Ensembl (popular in Europe)
      • +
    • Pros and cons of genome browsers +
        +
      • Pros +
          +
        • easy to use
          • +
        • regularly updated
          • +
        • automated annotation pipelines => fast to include new genomes
          • +
        • very powerful export utilities (BioMart in Ensembl)
          • +
        • API for local access
          • +
        • DAS (distributed annotation system) for data exchange
          • +
        • long term project, stable funding, likely not going away
          • +
        +
        • +
      • Cons +
          +
        • focus on vertebrates, few other genomes
          • +
        • complex db schema
          • +
        • popular, so can be slow
          • +
        +
        • +
      +
      • +
    +
    • +
+

Special ones:

+
    +
  • Comparative genomics databases +
      +
    • STRING (protein-protein interactions, focused on microbial genomes, maintained by von Mering group at UZH)
      • +
    • specialized on comparing genomes (at nucleotide-level, or gene-level)
      • +
    • to visualize evidence of selection (exons, regulatory sites, ...)
      • +
    • to infer past evolution of genomes (rearrangements, gains, losses, ...)
      • +
    • to establish gene histories (orthology, paralogy, synteny, ...)
      • +
    • often require extensive offline computation before they go online
      • +
    • some of their services also offered by generic genome browsers/sites.
      • +
    +
    • +
  • Organism-specific databases +
      +
    • Flybase, Wormbase, TAIR, SGD...
      • +
    • community driven, extensive manual input
      • +
    • specific terms, abbreviations, gene names...
      • +
    +
    • +
  • Specialized databases +
      +
    • IGSR: human population genetics
      • +
    • OMIM: known disease-causing mutations
      • +
    • KEGG: metabolic pathways and enzymes
      • +
    +
    • +
+
+ +
+ + +
+
+ + + +
+ + + + + + + + + + + + + + + + + + + + +
+ + diff --git a/23fs/fg/02_modern_genomics_ii.html b/23fs/fg/02_modern_genomics_ii.html new file mode 100644 index 0000000..0026a10 --- /dev/null +++ b/23fs/fg/02_modern_genomics_ii.html @@ -0,0 +1,305 @@ + + + + + + Modern Genomics II - Notes @ ETH Zürich + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ +
+ + + + + + + + +
+
+

Modern Genomics II

+

I cannot understand his accent...

+ +

Contents that (I think) are important

+

Linkage disequilibrium (LD)

+

Coefficient of linkage disequilibrium \( D \)

+

Given two loci \(A\) and \(B\) (can have allele \(A\) or \(a\), \(B\) or \(b\)), the coefficient of linkage disequilibrium \(D\) is defined as

+

\[ +D = \frac{P_{AB} - P_A P_B}{P_A P_B} +\]

+

Below shows two examples of \(D\) calculation.

+

LD example 1

+

\[ +D = \frac{P_{AB} - P_{A} P_{B}}{P_{A} P_{B}} = \frac{5}{12} - \frac{8}{12}\times\frac{6}{12} = \frac{1}{12} +\]

+

A and B are linked to some extent.

+

LD example 2

+

\[ +D = \frac{P_{AB} - P_{A} P_{B}}{P_{A} P_{B}} = \frac{6}{12} - \frac{8}{12}\times\frac{9}{12} = 0 +\]

+

Here A and B are not linked at all.

+

Basically we are testing whether P(A) and P(B) are independent.

+

Relative measures of LD

+
    +
  1. \(r^2 = \frac{D}{P_A P_a P_B P_b}\)
    2. +
  2. \(D' = \frac{D}{D_{\max}}\) if \(D\) is positive, \(D' = \frac{D}{D_{\min}}\) if \(D\) is negative
    3. +
+

Nucleotide diversity \(\pi\)

+

Average proportion of pairwise differences between the sequences

+

Give a multiple sequence alignment, \(\pi\) is defined as

+

\[ +\pi = \sum_{i < j} \frac{\pi_{ij}}{n_c} +\]

+

where \(n_c = \frac{n(n-1)}{2}\) is the number of pairwise comparisons, and \(\pi_{ij}\) is the proportion of differences between the \(i\)th and \(j\)th sequences.

+

Below shows an example of \(\pi\) calculation.

+

Nucleotide diversity example

+

\[ +\pi = \sum_{i < j} \frac{\pi_{ij}}{n_c} = \frac{\pi_{12} + \pi_{13} + \pi_{23}}{3} = 0.2 +\]

+

Basically just calculating the average number of differences in the matrix.

+

Course contents according to recording

+

Title: Applications of next-generation sequencing and other genomic techniques

+
    +
  1. Resequencing to identify genetic basis of phenotypic variation +
      +
    1. Outlier approach
      2. +
    2. Genome-wide association studies (GWAS) and linkage disequilibrium
      3. +
    +
    2. +
  2. Introduction to RNA-seq (transcriptome) focusing on genome duplication
    3. +
  3. Resequencing to detect signature of selection: nucleotide diversity
    4. +
+

Microbial community and metagenomics, ChIP-seq, epigenomics, whole genome assembly as reference

+
    +
  • Evolutionary functional genomics can... +
      +
    • identify ecologically relevant genes
      • +
    • inferring selection & population processes
      • +
    +
    • +
+ +
+ + +
+
+ + + +
+ + + + + + + + + + + + + + + + + + + + +
+ + diff --git a/23fs/fg/03_transcriptomics_i.html b/23fs/fg/03_transcriptomics_i.html new file mode 100644 index 0000000..e417633 --- /dev/null +++ b/23fs/fg/03_transcriptomics_i.html @@ -0,0 +1,719 @@ + + + + + + Transcriptomics I - Notes @ ETH Zürich + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ +
+ + + + + + + + +
+
+

Transcriptomics I

+

Unimportant text is grayed out but worth reading for fluency and context.

+ +

Motivation

+

We are interested in the expression of genes in a +cell. Altough proteins are the actors of genes instead of mRNA +transcripts, mRNAs transcripts are easier to measure because selection +has chosen them to convey the genetic message in a faithful way. Also there are +plenty of interesting non-coding RNAs.

+

RNA species

+

80% of the total RNA is rRNA. 14% is tRNA. Only 1-3% is mRNA. All other species +account for the remaining 1-3%.

+

RNA speciesPrevalence of RNA species

+

RNA selection methods

+

RNA selection methods

+
    +
  • A: total RNA +
      +
    • Unbiased estimation
      • +
    • Dominate by rRNA, not very informative
      • +
    +
    • +
  • B: ribosomal reduction/depletion +
      +
    • Use probes that bind to rRNA and pull them out
      • +
    • < 5% rRNA left
      • +
    +
    • +
  • C: poly-A selection +
      +
    • Use probes that bind to poly-A tails
      • +
    • Selects for mRNA, and also some long non-coding RNAs (because they also have +poly-A tails)
      • +
    +
    • +
  • D: cDNA capture +
      +
    • Design target probes that bind to a certain set of RNAs
      • +
    • Limited transcriptome coverage
      • +
    +
    • +
+

90% of transcriptome research utilize poly-A +selection; 5% of them go for ribosomal depletion because their mRNAs are of low +quality and fragmented. The rest 5% do have high-quality mRNAs but still go for +ribosomal depletion because they want to estimate other RNA species at the same +time.

+

Note: current illumina sequencers cannot sequence miRNAs (20-25nt) and mRNA +fragments (100-300nt) together (because of the large length discrepency)

+

RNA-seq experiment workflow overview

+

A typical RNA-seq experiment workflow is shown below.

+

Typical RNA-seq experiment

+

We can do either single-read sequencing or paired-end +sequencing (as is shown in the figure above) in the third step.

+

Paired-end sequencing

+

It can also be summarized into a flow diagram.

+

RNA-seq workflow diagram

+

The following sections will go into more details about each step.

+

RNA-seq experiment design

+
    +
  • RNA-seq experiments are implemented as comparative experiments
    • +
  • RNA-seq is used to measure the relative abundance (expression) of each +mRNA (gene) in a sample +
      +
    • sample: We +cannot sequence all the RNA fragments. Instead, we randomly select about 20M +fragments as a representation of the total RNA obtained. Note that we can +sample multiple times.
      • +
    +
    • +
  • RNA-seq can link gene expression to +
      +
    • genotype
      • +
    • phenotype
      • +
    • treatment response
      • +
    +
    • +
+

RNA-seq read mapping methods

+

Considerations

+

Ideally, the read mapping process is as simple as +sequencing the transcribed RNAs and then mapping the +sequences back to the genome to identify the gene expression.

+

However, in reality, the process is much more +complicated because current sequencers can only perform faithful sequencing +up to a couple of hundreds of bp (usually 200-800bp), and a typical mRNA is +2-3kb long. Thus, the mRNA needs to be first chopped into fragments and then +sequenced. When we do the mapping, we're mapping the chopped reads back to the +genome instead of the whole spliced sequences. The existence of alternative +splicing (protein isoforms) and sequencing errors makes the mapping +process even more complicated.

+

While discussing the mapping process, those +limitations and problems should be kept in mind.

+

How to map reads to a genome?

+
    +
  • Mapping algorithms must be +
      +
    • Fast +
        +
      • Thus usually find perfect or near-perfect (tolerating 1bp mismatch) match
        • +
      +
      • +
    • Able to handle SNPs, indels and sequencing errors
      • +
    +
    • +
+

We can always perform sequence alignment (here needs local +alignment/Smith-Waterman alignment). Of course the score matrix should be +good to determine the correct alignment. But this is slow because it requires +quadratic efforts.

+

What if we want to map billions of reads?

+
    +
  • Indexing method +
      +
    • Reads are aligned by index lookup instead of $O(n^2)$ seq comparison
      • +
    • Usually hashed so the lookup time is much faster
      • +
    • If lookup fails, actual sequence comparison is performed (more details on +this in next chapter)
      • +
    • Major aligners use the Burrows-Wheeler transform (BWT) to index +the reference genome +
        +
      • Very small. Even for the human genome the index +fits into 3GB RAM.
        • +
      +
      • +
    +
    • +
  • Example aligners + +
    • +
+

How to deal with SNPs and indels?

+
    +
  • SNPs +
      +
    • Can always be handled by performing real +Smith-Waterman alignment but expensive
      • +
    • At mismatched positions, try all possible bases and search the BWT index +again +
        +
      • Computing effort grows exponentially
        • +
      +
      • +
    • Gapped alignment +
        +
      • Chop reads into short segments (seeds)
        • +
      • align those seeds in a mismatch-free manner (typically using BWT +index lookup again)
        • +
      • stitch them back together
        • +
      • Might require multiple rounds of chopping
        • +
      +
      • +
    +
    • +
  • Indels +
      +
    • Can only be found with gapped alignment (described above), BWT lookup is +not enough
      • +
    +
    • +
+

How to deal with introns (basically very large insertions)?

+
    +
  • Approaches +
      +
    • Map directly to trapscript sequences (no intron) not to the genome +
        +
      • Pro: introns are not a problem
        • +
      • Cons: unknown genes/isoforms cannot be detected
        • +
      +
      • +
    • Spliced alignment to genome +
        +
      • Pro: finds reads from unknown gene loci or unknown isoforms
        • +
      • Con: larger search space, potentially more false positives, wrong +alignment to pseudogenes
        • +
      +
      • +
    • Combination of above
      • +
    +
    • +
  • Difference between spliced alignment and gapped alignment +
      +
    • Gapped alignment: longer gaps means high score penalty and lower score
      • +
    • Spliced alignment: long gaps at canonical splice-sites are allowed, +but lacking canonical splice-sites or gaps elsewhere (at non-canonical +splice sites) are penalized
      • +
    +
    • +
  • Pseudogenes +
      +
    • associated retrotransposed spliced sequence of a certain gene, thus +intron-free, and appears "exonic"
      • +
    • Have almost the same sequence as the original gene
      • +
    • Not functional because they do not have access to promotors so won't be +transcribed
      • +
    • Usually contain more mutations because there are no selection pressures to +keep them intact
      • +
    • Exonic reads will map to both the gene and its pseudogene, but likely +preferring gene placement due to lack of mutations
      • +
    • A spliced read could be incorrectly assigned to the pseudogene as it appears +to be exonic, preventing higher scoring spliced alignments from being +pursued
      • +
    +
    • +
+

Bowtie

+

Bowtie

+
    +
  • Step-by-step backward searching the suffix of the query sequence in +the BWT index +
      +
    • Exact matching
      • +
    +
    • +
  • Searched suffix appears consecutively in BWT
    • +
  • The size of range in BWT shrinks or remains the same
    • +
  • almost does not handle mismatches; a single mismatch will lead to +empty BWT range / failed index lookup +
      +
    • mismatches can come from +
        +
      • Sequencing error (illumina: $1/1000$)
        • +
      • True variation (SNPs, human mutation rate $\approx 1/10^4$
        • +
      +
      • +
    • mismatches are not rare events! at least 10% of >100nt reads
      • +
    +
    • +
  • Empty BWT range activates backtracking +
      +
    • All possible bases are tried at the mismatched position
      • +
    • Gapped alignment
      • +
    +
    • +
+

TopHat2

+

Handles mismatches by gapped alignment. It first performs (optional) +transcriptome alignment (exonic), and then performs genome +alignment for the unmapped reads. The unmapped reads in the second step are +multi-exon spanning reads and undergo spliced alignment by chopping the +reads into even shorter segments and splice site identification etc.

+
+

The figure is too complicated, not recommended to go into details but still +attached here for reference. TopHat2 pipeline

+
+

STAR

+

Direct alignment of non-contiguous sequences to the reference genome.

+
    +
  • First find Maximal Mappable Prefix (MMP) of the read +
      +
    • MMP is the longest prefix of the read that can be mapped to the reference +genome
      • +
    • MMP is found by searching the BWT index
      • +
    • Possible to tolerate a certain degree of mismatches using extend mode
      • +
    +
    • +
  • Stop extending MMP if MMP covers the whole read or encounters a mismatch
    • +
  • In the second case, find the MMP of the remaining suffix of the read
    • +
  • Repeat until the whole read is covered +
      +
    • Possible to use trim mode to get rid of A-tail or adapter sequence
      • +
    +
    • +
+STAR +

Quality control and reporting considerations after mapping

+

PHREAD quality

+
    +
  • Each called base is given a quality score $Q$
    • +
  • $Q = -10 \log_{10}(p)$ (PHRED score) +
      +
    • $p$ is the estimated probability of the base being called incorrectly
      • +
    • $Q$ is the negative log of the probability +
        +
      • Q-score = 10: prob = 0.1
        • +
      • Q-score = 20: prob = 0.01
        • +
      • Q-score = 30: prob = 0.001
        • +
      +
      • +
    • Q30 is often used as a cutoff for high quality reads
      • +
    +
    • +
  • How to use: downweight the low-quality bases when computing the alignment +score
    • +
  • First introduced for capillary sequencers
    • +
  • PHRED scores are determined by the sequencer that +directly rates how reliable the measured signal is
    • +
+

Read trimming

+

Not all parts of the read are useful for alignment. It is common to trim the +reads.

+
    +
  • Reasons for trimming: +
      +
    • Systemetic errors of sequencer +
        +
      • Illumina sequencers have high error rate at the first few bases
        • +
      • Basically all sequencers have increasing error rate towards the end of the +read
        • +
      +
      • +
    • Adapter trimming +
        +
      • If the inserted DNA/RNA fragment is too short, the read will contain part +of the adapter (since the sequencer generally will sequence 100bp at each +end)
        • +
      • Can be challenging if: +
          +
        • The inserted sequence is 90-100bp -- the incorporated adapter sequence +will only be a few bp long
          • +
        • The read has many sequencing errors
          • +
        +
        • +
      +
      • +
    • 3'-bias / degradation +
        +
      • The 3' end of the read is generally more likely to be degraded than the 5' +end
        • +
      • Depending on RNA degradation and extration protocols reads may not be +equally distributed along the transcripts
        • +
      +
      • +
    +
    • +
  • Trimming methods +
      +
    • Hard trimming: trim a fixed number of bases from the beginning and/or +end
      • +
    • Quality trimming: cut the end of the read as soon as the base quality +drops below a threshold
      • +
    • Soft trimming: trim the read that cannot be aligned to the reference +genome
      • +
    +
    • +
+

Multiple alignments and report considerations

+
    +
  • A read may have multiple valid alignments with identical or similarly good +alignment scores +
      +
    • Aligners may use different reporting strategies: +
        +
      • Randomly select one alignment from the top-scoring alignments
        • +
      • Report all alignments that are within delta of the +top-scoring alignment; clip if more than $N_{max}$ alignments are found
        • +
      • Report only alignments if they are unique (no other alignment within +delta of the alignment score)
        • +
      • Do not report anything if more than $N_{max}$ valid alignments are found
        • +
      • …
        • +
      +
      • +
    +
    • +
  • Whether a read has a unique alignment depends on +
      +
    • the read sequence and the sequence homology of the organism
      • +
    • the search algorithm of the aligner
      • +
    +
    • +
  • Whether a read has a single reported alignment depends additionally on +
      +
    • the reporting options strategy of the aligner
      • +
    +
    • +
+

Expression quantification

+
    +
  • Expression quantification on +
      +
    • Gene level +
        +
      • Reads belong to a gene locus
        • +
      +
      • +
    • Isoform level +
        +
      • Reads belong to an isoform
        • +
      +
      • +
    +
    • +
+

How to count reads?

+
    +
  • Unique mapped reads +
      +
    • Multi-reads are ignored – potentially biased quantification
      • +
    +
    • +
  • All mapped reads +
      +
    • Assignment of multi-reads need abundance estimation of overlapped +genes/isoforms
      • +
    +
    • +
+

Read counting

+

EM estimation

+
    +
  • General steps +
      +
    1. Estimate abundances based on uniquely mapping reads only
      2. +
    2. For each multi-read, divide it between the transcripts to which it maps, proportionally to their abundances estimated in the first step
      3. +
    3. Recompute abundances based on updated counts for each transcript +r.
      4. +
    4. Continue with Step 2
      5. +
    +
    • +
  • Model the sequencing and analysis process with a likelihood function
    • +
  • E-step: Compute expected read counts given current expression levels
    • +
  • M-step: Compute expression values maximizing likelihood given expected read counts
    • +
+

Alignment-free RNA-seq quantification

+

Instead of building BWT, we build hashed k-mer index based on known +transcriptome, and search the k-mers in the reads to map and compute abundance.

+

Easier to understand through side-by-side comparison with the traditional +alignment dependent method:

+

Alignment dependent v.s. alignment free

+

While allocating k-mer to transcript, we try to make each transcript covered +as uniformly as possible.

+
    +
  • Pros +
      +
    • Accurate and fast in quantifying KNOWN TRANSCRIPTS
      • +
    • Counts can be aggregated to get gene-level quantification
      • +
    +
    • +
  • Cons +
      +
    • Less well annotated genomes – less accurate results
      • +
    • No alignments – no information about SNPs
      • +
    • Transcript coverage is not uniform
      • +
    +
    • +
+

Normalization

+ +
+ + +
+
+ + + +
+ + + + + + + + + + + + + + + + + + + + +
+ + diff --git a/23fs/fg/04_transcriptomics_ii.html b/23fs/fg/04_transcriptomics_ii.html new file mode 100644 index 0000000..91408cf --- /dev/null +++ b/23fs/fg/04_transcriptomics_ii.html @@ -0,0 +1,417 @@ + + + + + + Transcriptomics II - Notes @ ETH Zürich + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ +
+ + + + + + + + +
+
+

Transcriptomics II

+ + +

Methods of Exploratory Data Analysis

+

Typical shape of data we have in hand: a data matrix.

+

Data matrix

+

where the columns are the samples and the rows are the features (usually gene expressions). (It can be the other way around, but this is the most common case.)

+
    +
  • Clustering +
      +
    • Hierarchical clustering
      • +
    • k-means clustering
      • +
    +
    • +
  • Dimensionality reduction +
      +
    • Matrix Factorization +
        +
      • PCA
        • +
      • MDS (Multidimensional Scaling)
        • +
      +
      • +
    • Graph-based methods +
        +
      • t-SNE
        • +
      • UMAP
        • +
      +
      • +
    +
    • +
+

Clustering

+
    +
  • Goals +
      +
    • group similar samples +
        +
      • evaluate similarity between expression profiles of the samples
        • +
      • test if similarities match the experimental design and effect sizes
        • +
      • test if variations within condition is smaller than between conditions
        • +
      • outliers detection
        • +
      +
      • +
    • group similar genes +
        +
      • guilt by association: infer functions of unknown genes from known genes with the same expression pattern (co-expression)
        • +
      +
      • +
    +
    • +
+

Distance measures

+

To cluster samples, we need to first define a "distance" measure between samples.

+

Commonly used distance measures:

+
    +
  • Euclidean distance (typically for clustering samples) +
      +
    • Euclidean distance of two profiles $\mathbf{x}$ and $\mathbf{y}$ with $p$ genes (i.e. the distance between two $p$-dimensional vectors $\mathbf{x}$ and $\mathbf{y}$)
      • +
    • $d(\mathbf{x}, \mathbf{y}) = \sqrt{\sum_{i=1}^{p} \left(x_i - y_i\right)^2}$
      • +
    • Expression values MUST BE LOG SCALE
      • +
    +
    • +
  • $1 - \text{corr}(\mathbf{x}, \mathbf{y})$ (typically for clustering genes) +
      +
    • Correlation coefficient of two profiles $\mathbf{x}$ and $\mathbf{y}$ with $p$ samples
      • +
    • $\text{corr}(\mathbf{x}, \mathbf{y}) = \frac{\sum_{i=1}^{p}(x_i - \bar{x})(y_i - \bar{y})}{\sqrt{\sum_{i=1}^{p}(x_i - \bar{x})^2 \cdot \sum_{i-1}^{p}(y_i - \bar{y})^2}}$
      • +
    • $\bar{x} = \frac{1}{p}\sum_{i=1}^{p}x_i$
      • +
    • $\bar{y} = \frac{1}{p}\sum_{i=1}^{p}y_i$
      • +
    +
    • +
+

Hierarchical Clustering

+

Algorithm:

+
    +
  1. Compute the distance matrix ($n \times (n - 1) / 2 \rightarrow O(n^2)$) between all samples
    2. +
  2. Find pair with minimal distance and merge them
    3. +
  3. Update the distance matrix
    4. +
  4. Repeat 2-3 until all samples are merged
    5. +
+

Parameters:

+
    +
  • distance measure for samples +
      +
    • usually $1 - \text{corr}(\mathbf{x}, \mathbf{y})$ for gene expression
      • +
    +
    • +
  • distance measure for clusters (linkage rule) +
      +
    • Single linkage: minimum distance between any elements of the two clusters
      • +
    • Complete linkage: maximum distance between any elements of the two clusters
      • +
    • Average linkage: average distance between all elements of the two clusters
      • +
    • Ward's linkage: minimal increase in intra-cluster variance
      • +
    +
    • +
+

Input:

+
    +
  • distance matrix +
      +
    • The linkage can be derived directly from the distance matrix.
      • +
    • Hence clustering algorithm only needs the distrance matrix as input, not the measurements individually.
      • +
    +
    • +
+

k-means Clustering

+

Algorithm:

+
    +
  1. Randomly assign each sample to one of the $k$ clusters
    2. +
  2. Compute the centroid (cluster center, average of the assigned samples) of each cluster
    3. +
  3. Assign each sample to the cluster with the closest centroid
    4. +
  4. Repeat 2-3 until convergence or a maximum number of iterations
    5. +
+

Parameters:

+
    +
  • number of clusters $k$
    • +
  • distance measure for samples
    • +
+

Input:

+
    +
  • data matrix (cannot directly use distance matrix)
    • +
+

This method minimizes the intra-cluster variance.

+

Choice of $k$ affects the result.

+

Comparison of Hierarchical Clustering and k-means Clustering

+
+ + +
Hierarchical Clusteringk-means Clustering
Computing time$O(n^2 \log (n))$$O(n \cdot k \cdot t)$
  • $t$: number of iterations
  • $k$: number of clusters
Memory$O(n^2)$$O(n \cdot k)$
+
+

When clustering large numbers of genes (>1e4, hierarchical clustering is not practical

+

Dimensionality Reduction

+

Principal Component Analysis (PCA)

+

Goal: Find a new coordinate system such that the first axis (principal component) captures the most variance, the second axis captures the second most variance, and so on.

+

The data is linearly transformed to a new coordinate system.

+

t-SNE

+

Algorithm:

+
    +
  1. In the high-dimensional space, create a probability distribution that dictates how likely two points are to be neighbors.
    2. +
  2. Recreate a low dimensional space that follows the same probability distribution as best as possible.
    3. +
+

How to find the best low-dimensional representation:

+
    +
  • preserve the pairwise distances between neighboring points in the high-dimensional space
    • +
  • non-linear, different transformations on different regions
    • +
+

Characteristic:

+
    +
  • Powerful, but need to fiddle with random seed and perplexity
    • +
  • Non-deterministic
    • +
+

UMAP

+

Uniform Manifold Approximation and Projection

+

Approach: Find for each point the neighbors and build simplices (simplex: a generalization of the concept of a triangle or tetrahedron to arbitrary dimensions) and then optimize the low-dimensional representation to preserve the simplices.

+

Differential Expression Analysis

+ +
+ + +
+
+ + + +
+ + + + + + + + + + + + + + + + + + + + +
+ + diff --git a/23fs/fg/functional_genomics.html b/23fs/fg/functional_genomics.html new file mode 100644 index 0000000..a7c477c --- /dev/null +++ b/23fs/fg/functional_genomics.html @@ -0,0 +1,248 @@ + + + + + + Functional Genomics - Notes @ ETH Zürich + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ +
+ + + + + + + + +
+
+

Functional Genomics

+

A course collectively taught by multiple professors. Multiple-choice exam, lots of memorization.

+

Table of Contents

+ + + +
+ + +
+
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+ +// Fix back button cache problem +window.onunload = function () { }; + +// Global variable, shared between modules +function playground_text(playground, hidden = true) { + let code_block = playground.querySelector("code"); + + if (window.ace && code_block.classList.contains("editable")) { + let editor = window.ace.edit(code_block); + return editor.getValue(); + } else if (hidden) { + return code_block.textContent; + } else { + return code_block.innerText; + } +} + +(function codeSnippets() { + function fetch_with_timeout(url, options, timeout = 6000) { + return Promise.race([ + fetch(url, options), + new Promise((_, reject) => setTimeout(() => reject(new Error('timeout')), timeout)) + ]); + } + + var playgrounds = Array.from(document.querySelectorAll(".playground")); + if (playgrounds.length > 0) { + fetch_with_timeout("https://play.rust-lang.org/meta/crates", { + headers: { + 'Content-Type': "application/json", + }, + method: 'POST', + mode: 'cors', + }) + .then(response => response.json()) + .then(response => { + // get list of crates available in the rust playground + let playground_crates = response.crates.map(item => item["id"]); + playgrounds.forEach(block => handle_crate_list_update(block, playground_crates)); + }); + } + + function handle_crate_list_update(playground_block, playground_crates) { + // update the play buttons after receiving the response + update_play_button(playground_block, playground_crates); + + // and install on change listener to dynamically update ACE editors + if (window.ace) { + let code_block = playground_block.querySelector("code"); + if (code_block.classList.contains("editable")) { + let editor = window.ace.edit(code_block); + editor.addEventListener("change", function (e) { + update_play_button(playground_block, playground_crates); + }); + // add Ctrl-Enter command to execute rust code + editor.commands.addCommand({ + name: "run", + bindKey: { + win: "Ctrl-Enter", + mac: "Ctrl-Enter" + }, + exec: _editor => run_rust_code(playground_block) + }); + } + } + } + + // updates the visibility of play button based on `no_run` class and + // used crates vs ones available on https://play.rust-lang.org + function update_play_button(pre_block, playground_crates) { + var play_button = pre_block.querySelector(".play-button"); + + // skip if code is `no_run` + if (pre_block.querySelector('code').classList.contains("no_run")) { + play_button.classList.add("hidden"); + return; + } + + // get list of `extern crate`'s from snippet + var txt = playground_text(pre_block); + var re = /extern\s+crate\s+([a-zA-Z_0-9]+)\s*;/g; + var snippet_crates = []; + var item; + while (item = re.exec(txt)) { + snippet_crates.push(item[1]); + } + + // check if all used crates are available on play.rust-lang.org + var all_available = snippet_crates.every(function (elem) { + return playground_crates.indexOf(elem) > -1; + }); + + if (all_available) { + play_button.classList.remove("hidden"); + } else { + play_button.classList.add("hidden"); + } + } + + function run_rust_code(code_block) { + var result_block = code_block.querySelector(".result"); + if (!result_block) { + result_block = document.createElement('code'); + result_block.className = 'result hljs language-bash'; + + code_block.append(result_block); + } + + let text = playground_text(code_block); + let classes = code_block.querySelector('code').classList; + let edition = "2015"; + if(classes.contains("edition2018")) { + edition = "2018"; + } else if(classes.contains("edition2021")) { + edition = "2021"; + } + var params = { + version: "stable", + optimize: "0", + code: text, + edition: edition + }; + + if (text.indexOf("#![feature") !== -1) { + params.version = "nightly"; + } + + result_block.innerText = "Running..."; + + fetch_with_timeout("https://play.rust-lang.org/evaluate.json", { + headers: { + 'Content-Type': "application/json", + }, + method: 'POST', + mode: 'cors', + body: JSON.stringify(params) + }) + .then(response => response.json()) + .then(response => { + if (response.result.trim() === '') { + result_block.innerText = "No output"; + result_block.classList.add("result-no-output"); + } else { + result_block.innerText = response.result; + result_block.classList.remove("result-no-output"); + } + }) + .catch(error => result_block.innerText = "Playground Communication: " + error.message); + } + + // Syntax highlighting Configuration + hljs.configure({ + tabReplace: ' ', // 4 spaces + languages: [], // Languages used for auto-detection + }); + + let code_nodes = Array + .from(document.querySelectorAll('code')) + // Don't highlight `inline code` blocks in headers. + .filter(function (node) {return !node.parentElement.classList.contains("header"); }); + + if (window.ace) { + // language-rust class needs to be removed for editable + // blocks or highlightjs will capture events + code_nodes + .filter(function (node) {return node.classList.contains("editable"); }) + .forEach(function (block) { block.classList.remove('language-rust'); }); + + code_nodes + .filter(function (node) {return !node.classList.contains("editable"); }) + .forEach(function (block) { hljs.highlightBlock(block); }); + } else { + code_nodes.forEach(function (block) { hljs.highlightBlock(block); }); + } + + // Adding the hljs class gives code blocks the color css + // even if highlighting doesn't apply + code_nodes.forEach(function (block) { block.classList.add('hljs'); }); + + Array.from(document.querySelectorAll("code.hljs")).forEach(function (block) { + + var lines = Array.from(block.querySelectorAll('.boring')); + // If no lines were hidden, return + if (!lines.length) { return; } + block.classList.add("hide-boring"); + + var buttons = document.createElement('div'); + buttons.className = 'buttons'; + buttons.innerHTML = ""; + + // add expand button + var pre_block = block.parentNode; + pre_block.insertBefore(buttons, pre_block.firstChild); + + pre_block.querySelector('.buttons').addEventListener('click', function (e) { + if (e.target.classList.contains('fa-eye')) { + e.target.classList.remove('fa-eye'); + e.target.classList.add('fa-eye-slash'); + e.target.title = 'Hide lines'; + e.target.setAttribute('aria-label', e.target.title); + + block.classList.remove('hide-boring'); + } else if (e.target.classList.contains('fa-eye-slash')) { + e.target.classList.remove('fa-eye-slash'); + e.target.classList.add('fa-eye'); + e.target.title = 'Show hidden lines'; + e.target.setAttribute('aria-label', e.target.title); + + block.classList.add('hide-boring'); + } + }); + }); + + if (window.playground_copyable) { + Array.from(document.querySelectorAll('pre code')).forEach(function (block) { + var pre_block = block.parentNode; + if (!pre_block.classList.contains('playground')) { + var buttons = pre_block.querySelector(".buttons"); + if (!buttons) { + buttons = document.createElement('div'); + buttons.className = 'buttons'; + pre_block.insertBefore(buttons, pre_block.firstChild); + } + + var clipButton = document.createElement('button'); + clipButton.className = 'fa fa-copy clip-button'; + clipButton.title = 'Copy to clipboard'; + clipButton.setAttribute('aria-label', clipButton.title); + clipButton.innerHTML = ''; + + buttons.insertBefore(clipButton, buttons.firstChild); + } + }); + } + + // Process playground code blocks + Array.from(document.querySelectorAll(".playground")).forEach(function (pre_block) { + // Add play button + var buttons = pre_block.querySelector(".buttons"); + if (!buttons) { + buttons = document.createElement('div'); + buttons.className = 'buttons'; + pre_block.insertBefore(buttons, pre_block.firstChild); + } + + var runCodeButton = document.createElement('button'); + runCodeButton.className = 'fa fa-play play-button'; + runCodeButton.hidden = true; + runCodeButton.title = 'Run this code'; + runCodeButton.setAttribute('aria-label', runCodeButton.title); + + buttons.insertBefore(runCodeButton, buttons.firstChild); + runCodeButton.addEventListener('click', function (e) { + run_rust_code(pre_block); + }); + + if (window.playground_copyable) { + var copyCodeClipboardButton = document.createElement('button'); + copyCodeClipboardButton.className = 'fa fa-copy clip-button'; + copyCodeClipboardButton.innerHTML = ''; + copyCodeClipboardButton.title = 'Copy to clipboard'; + copyCodeClipboardButton.setAttribute('aria-label', copyCodeClipboardButton.title); + + buttons.insertBefore(copyCodeClipboardButton, buttons.firstChild); + } + + let code_block = pre_block.querySelector("code"); + if (window.ace && code_block.classList.contains("editable")) { + var undoChangesButton = document.createElement('button'); + undoChangesButton.className = 'fa fa-history reset-button'; + undoChangesButton.title = 'Undo changes'; + undoChangesButton.setAttribute('aria-label', undoChangesButton.title); + + buttons.insertBefore(undoChangesButton, buttons.firstChild); + + undoChangesButton.addEventListener('click', function () { + let editor = window.ace.edit(code_block); + editor.setValue(editor.originalCode); + editor.clearSelection(); + }); + } + }); +})(); + +(function themes() { + var html = document.querySelector('html'); + var themeToggleButton = document.getElementById('theme-toggle'); + var themePopup = document.getElementById('theme-list'); + var themeColorMetaTag = document.querySelector('meta[name="theme-color"]'); + var stylesheets = { + ayuHighlight: document.querySelector("[href$='ayu-highlight.css']"), + tomorrowNight: document.querySelector("[href$='tomorrow-night.css']"), + highlight: document.querySelector("[href$='highlight.css']"), + }; + + function showThemes() { + themePopup.style.display = 'block'; + themeToggleButton.setAttribute('aria-expanded', true); + themePopup.querySelector("button#" + get_theme()).focus(); + } + + function updateThemeSelected() { + themePopup.querySelectorAll('.theme-selected').forEach(function (el) { + el.classList.remove('theme-selected'); + }); + themePopup.querySelector("button#" + get_theme()).classList.add('theme-selected'); + } + + function hideThemes() { + themePopup.style.display = 'none'; + themeToggleButton.setAttribute('aria-expanded', false); + themeToggleButton.focus(); + } + + function get_theme() { + var theme; + try { theme = localStorage.getItem('mdbook-theme'); } catch (e) { } + if (theme === null || theme === undefined) { + return default_theme; + } else { + return theme; + } + } + + function set_theme(theme, store = true) { + let ace_theme; + + if (theme == 'coal' || theme == 'navy') { + stylesheets.ayuHighlight.disabled = true; + stylesheets.tomorrowNight.disabled = false; + stylesheets.highlight.disabled = true; + + ace_theme = "ace/theme/tomorrow_night"; + } else if (theme == 'ayu') { + stylesheets.ayuHighlight.disabled = false; + stylesheets.tomorrowNight.disabled = true; + stylesheets.highlight.disabled = true; + ace_theme = "ace/theme/tomorrow_night"; + } else { + stylesheets.ayuHighlight.disabled = true; + stylesheets.tomorrowNight.disabled = true; + stylesheets.highlight.disabled = false; + ace_theme = "ace/theme/dawn"; + } + + setTimeout(function () { + themeColorMetaTag.content = getComputedStyle(document.documentElement).backgroundColor; + }, 1); + + if (window.ace && window.editors) { + window.editors.forEach(function (editor) { + editor.setTheme(ace_theme); + }); + } + + var previousTheme = get_theme(); + + if (store) { + try { localStorage.setItem('mdbook-theme', theme); } catch (e) { } + } + + html.classList.remove(previousTheme); + html.classList.add(theme); + updateThemeSelected(); + } + + // Set theme + var theme = get_theme(); + + set_theme(theme, false); + + themeToggleButton.addEventListener('click', function () { + if (themePopup.style.display === 'block') { + hideThemes(); + } else { + showThemes(); + } + }); + + themePopup.addEventListener('click', function (e) { + var theme; + if (e.target.className === "theme") { + theme = e.target.id; + } else if (e.target.parentElement.className === "theme") { + theme = e.target.parentElement.id; + } else { + return; + } + set_theme(theme); + }); + + themePopup.addEventListener('focusout', function(e) { + // e.relatedTarget is null in Safari and Firefox on macOS (see workaround below) + if (!!e.relatedTarget && !themeToggleButton.contains(e.relatedTarget) && !themePopup.contains(e.relatedTarget)) { + hideThemes(); + } + }); + + // Should not be needed, but it works around an issue on macOS & iOS: https://github.com/rust-lang/mdBook/issues/628 + document.addEventListener('click', function(e) { + if (themePopup.style.display === 'block' && !themeToggleButton.contains(e.target) && !themePopup.contains(e.target)) { + hideThemes(); + } + }); + + document.addEventListener('keydown', function (e) { + if (e.altKey || e.ctrlKey || e.metaKey || e.shiftKey) { return; } + if (!themePopup.contains(e.target)) { return; } + + switch (e.key) { + case 'Escape': + e.preventDefault(); + hideThemes(); + break; + case 'ArrowUp': + e.preventDefault(); + var li = document.activeElement.parentElement; + if (li && li.previousElementSibling) { + li.previousElementSibling.querySelector('button').focus(); + } + break; + case 'ArrowDown': + e.preventDefault(); + var li = document.activeElement.parentElement; + if (li && li.nextElementSibling) { + li.nextElementSibling.querySelector('button').focus(); + } + break; + case 'Home': + e.preventDefault(); + themePopup.querySelector('li:first-child button').focus(); + break; + case 'End': + e.preventDefault(); + themePopup.querySelector('li:last-child button').focus(); + break; + } + }); +})(); + +(function sidebar() { + var body = document.querySelector("body"); + var sidebar = document.getElementById("sidebar"); + var sidebarLinks = document.querySelectorAll('#sidebar a'); + var sidebarToggleButton = document.getElementById("sidebar-toggle"); + var sidebarResizeHandle = document.getElementById("sidebar-resize-handle"); + var firstContact = null; + + function showSidebar() { + body.classList.remove('sidebar-hidden') + body.classList.add('sidebar-visible'); + Array.from(sidebarLinks).forEach(function (link) { + link.setAttribute('tabIndex', 0); + }); + sidebarToggleButton.setAttribute('aria-expanded', true); + sidebar.setAttribute('aria-hidden', false); + try { localStorage.setItem('mdbook-sidebar', 'visible'); } catch (e) { } + } + + + var sidebarAnchorToggles = document.querySelectorAll('#sidebar a.toggle'); + + function toggleSection(ev) { + ev.currentTarget.parentElement.classList.toggle('expanded'); + } + + Array.from(sidebarAnchorToggles).forEach(function (el) { + el.addEventListener('click', toggleSection); + }); + + function hideSidebar() { + body.classList.remove('sidebar-visible') + body.classList.add('sidebar-hidden'); + Array.from(sidebarLinks).forEach(function (link) { + link.setAttribute('tabIndex', -1); + }); + sidebarToggleButton.setAttribute('aria-expanded', false); + sidebar.setAttribute('aria-hidden', true); + try { localStorage.setItem('mdbook-sidebar', 'hidden'); } catch (e) { } + } + + // Toggle sidebar + sidebarToggleButton.addEventListener('click', function sidebarToggle() { + if (body.classList.contains("sidebar-hidden")) { + var current_width = parseInt( + document.documentElement.style.getPropertyValue('--sidebar-width'), 10); + if (current_width < 150) { + document.documentElement.style.setProperty('--sidebar-width', '150px'); + } + showSidebar(); + } else if (body.classList.contains("sidebar-visible")) { + hideSidebar(); + } else { + if (getComputedStyle(sidebar)['transform'] === 'none') { + hideSidebar(); + } else { + showSidebar(); + } + } + }); + + sidebarResizeHandle.addEventListener('mousedown', initResize, false); + + function initResize(e) { + window.addEventListener('mousemove', resize, false); + window.addEventListener('mouseup', stopResize, false); + body.classList.add('sidebar-resizing'); + } + function resize(e) { + var pos = (e.clientX - sidebar.offsetLeft); + if (pos < 20) { + hideSidebar(); + } else { + if (body.classList.contains("sidebar-hidden")) { + showSidebar(); + } + pos = Math.min(pos, window.innerWidth - 100); + document.documentElement.style.setProperty('--sidebar-width', pos + 'px'); + } + } + //on mouseup remove windows functions mousemove & mouseup + function stopResize(e) { + body.classList.remove('sidebar-resizing'); + window.removeEventListener('mousemove', resize, false); + window.removeEventListener('mouseup', stopResize, false); + } + + document.addEventListener('touchstart', function (e) { + firstContact = { + x: e.touches[0].clientX, + time: Date.now() + }; + }, { passive: true }); + + document.addEventListener('touchmove', function (e) { + if (!firstContact) + return; + + var curX = e.touches[0].clientX; + var xDiff = curX - firstContact.x, + tDiff = Date.now() - firstContact.time; + + if (tDiff < 250 && Math.abs(xDiff) >= 150) { + if (xDiff >= 0 && firstContact.x < Math.min(document.body.clientWidth * 0.25, 300)) + showSidebar(); + else if (xDiff < 0 && curX < 300) + hideSidebar(); + + firstContact = null; + } + }, { passive: true }); +})(); + +(function chapterNavigation() { + document.addEventListener('keydown', function (e) { + if (e.altKey || e.ctrlKey || e.metaKey || e.shiftKey) { return; } + if (window.search && window.search.hasFocus()) { return; } + var html = document.querySelector('html'); + + function next() { + var nextButton = document.querySelector('.nav-chapters.next'); + if (nextButton) { + window.location.href = nextButton.href; + } + } + function prev() { + var previousButton = document.querySelector('.nav-chapters.previous'); + if (previousButton) { + window.location.href = previousButton.href; + } + } + switch (e.key) { + case 'ArrowRight': + e.preventDefault(); + if (html.dir == 'rtl') { + prev(); + } else { + next(); + } + break; + case 'ArrowLeft': + e.preventDefault(); + if (html.dir == 'rtl') { + next(); + } else { + prev(); + } + break; + } + }); +})(); + +(function clipboard() { + var clipButtons = document.querySelectorAll('.clip-button'); + + function hideTooltip(elem) { + elem.firstChild.innerText = ""; + elem.className = 'fa fa-copy clip-button'; + } + + function showTooltip(elem, msg) { + elem.firstChild.innerText = msg; + elem.className = 'fa fa-copy tooltipped'; + } + + var clipboardSnippets = new ClipboardJS('.clip-button', { + text: function (trigger) { + hideTooltip(trigger); + let playground = trigger.closest("pre"); + return playground_text(playground, false); + } + }); + + Array.from(clipButtons).forEach(function (clipButton) { + clipButton.addEventListener('mouseout', function (e) { + hideTooltip(e.currentTarget); + }); + }); + + clipboardSnippets.on('success', function (e) { + e.clearSelection(); + showTooltip(e.trigger, "Copied!"); + }); + + clipboardSnippets.on('error', function (e) { + showTooltip(e.trigger, "Clipboard error!"); + }); +})(); + +(function scrollToTop () { + var menuTitle = document.querySelector('.menu-title'); + + menuTitle.addEventListener('click', function () { + document.scrollingElement.scrollTo({ top: 0, behavior: 'smooth' }); + }); +})(); + +(function controllMenu() { + var menu = document.getElementById('menu-bar'); + + (function controllPosition() { + var scrollTop = document.scrollingElement.scrollTop; + var prevScrollTop = scrollTop; + var minMenuY = -menu.clientHeight - 50; + // When the script loads, the page can be at any scroll (e.g. if you reforesh it). + menu.style.top = scrollTop + 'px'; + // Same as parseInt(menu.style.top.slice(0, -2), but faster + var topCache = menu.style.top.slice(0, -2); + menu.classList.remove('sticky'); + var stickyCache = false; // Same as menu.classList.contains('sticky'), but faster + document.addEventListener('scroll', function () { + scrollTop = Math.max(document.scrollingElement.scrollTop, 0); + // `null` means that it doesn't need to be updated + var nextSticky = null; 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+} + +/* + body-container is necessary because mobile browsers don't seem to like + overflow-x on the body tag when there is a tag. +*/ +#body-container { + /* + This is used when the sidebar pushes the body content off the side of + the screen on small screens. Without it, dragging on mobile Safari + will want to reposition the viewport in a weird way. + */ + overflow-x: clip; +} + +/* Menu Bar */ + +#menu-bar, +#menu-bar-hover-placeholder { + z-index: 101; + margin: auto calc(0px - var(--page-padding)); +} +#menu-bar { + position: relative; + display: flex; + flex-wrap: wrap; + background-color: var(--bg); + border-block-end-color: var(--bg); + border-block-end-width: 1px; + border-block-end-style: solid; +} +#menu-bar.sticky, +.js #menu-bar-hover-placeholder:hover + #menu-bar, +.js #menu-bar:hover, +.js.sidebar-visible #menu-bar { + position: -webkit-sticky; + position: sticky; + top: 0 !important; +} +#menu-bar-hover-placeholder { + position: sticky; + position: -webkit-sticky; + top: 0; + height: var(--menu-bar-height); +} +#menu-bar.bordered { + border-block-end-color: var(--table-border-color); +} +#menu-bar i, #menu-bar .icon-button { + position: relative; + padding: 0 8px; + z-index: 10; + line-height: var(--menu-bar-height); + cursor: pointer; + transition: color 0.5s; +} +@media only screen and (max-width: 420px) { + #menu-bar i, #menu-bar .icon-button { + padding: 0 5px; + } +} + +.icon-button { + border: none; + background: none; + padding: 0; + color: inherit; +} +.icon-button i { + margin: 0; +} + +.right-buttons { + margin: 0 15px; +} +.right-buttons a { + text-decoration: none; +} + +.left-buttons { + display: flex; + margin: 0 5px; +} +.no-js .left-buttons button { + display: none; +} + +.menu-title { + display: inline-block; + font-weight: 200; + font-size: 2.4rem; + line-height: var(--menu-bar-height); + text-align: center; + margin: 0; + flex: 1; + white-space: nowrap; + overflow: hidden; + text-overflow: ellipsis; +} +.js .menu-title { + cursor: pointer; +} + +.menu-bar, +.menu-bar:visited, +.nav-chapters, +.nav-chapters:visited, +.mobile-nav-chapters, +.mobile-nav-chapters:visited, +.menu-bar .icon-button, +.menu-bar a i { + color: var(--icons); +} + +.menu-bar i:hover, +.menu-bar .icon-button:hover, +.nav-chapters:hover, +.mobile-nav-chapters i:hover { + color: var(--icons-hover); +} + +/* Nav Icons */ + +.nav-chapters { + font-size: 2.5em; + text-align: center; + text-decoration: none; + + position: fixed; + top: 0; + bottom: 0; + margin: 0; + max-width: 150px; + min-width: 90px; + + display: flex; + justify-content: center; + align-content: center; + flex-direction: column; + + transition: color 0.5s, background-color 0.5s; +} + +.nav-chapters:hover { + text-decoration: none; + background-color: var(--theme-hover); + transition: background-color 0.15s, color 0.15s; +} + +.nav-wrapper { + margin-block-start: 50px; + display: none; +} + +.mobile-nav-chapters { + font-size: 2.5em; + text-align: center; + text-decoration: none; + width: 90px; + border-radius: 5px; + background-color: var(--sidebar-bg); +} + +/* Only Firefox supports flow-relative values */ +.previous { float: left; } +[dir=rtl] .previous { float: right; } + +/* Only Firefox supports flow-relative values */ +.next { + float: right; + right: var(--page-padding); +} +[dir=rtl] .next { + float: left; + right: unset; + left: var(--page-padding); +} + +/* Use the correct buttons for RTL layouts*/ +[dir=rtl] .previous i.fa-angle-left:before {content:"\f105";} +[dir=rtl] .next i.fa-angle-right:before { content:"\f104"; } + +@media only screen and (max-width: 1080px) { + .nav-wide-wrapper { display: none; } + .nav-wrapper { display: block; } +} + +/* sidebar-visible */ +@media only screen and (max-width: 1380px) { + #sidebar-toggle-anchor:checked ~ .page-wrapper .nav-wide-wrapper { display: none; } + #sidebar-toggle-anchor:checked ~ .page-wrapper .nav-wrapper { display: block; } +} + +/* Inline code */ + +:not(pre) > .hljs { + display: inline; + padding: 0.1em 0.3em; + border-radius: 3px; +} + +:not(pre):not(a) > .hljs { + color: var(--inline-code-color); + overflow-x: initial; +} + +a:hover > .hljs { + text-decoration: underline; +} + +pre { + position: relative; +} +pre > .buttons { + position: absolute; + z-index: 100; + right: 0px; + top: 2px; + margin: 0px; + padding: 2px 0px; + + color: var(--sidebar-fg); + cursor: pointer; + visibility: hidden; + opacity: 0; + transition: visibility 0.1s linear, opacity 0.1s linear; +} +pre:hover > .buttons { + visibility: visible; + opacity: 1 +} +pre > .buttons :hover { + color: var(--sidebar-active); + border-color: var(--icons-hover); + background-color: var(--theme-hover); +} +pre > .buttons i { + margin-inline-start: 8px; +} +pre > .buttons button { + cursor: inherit; + margin: 0px 5px; + padding: 3px 5px; + font-size: 14px; + + border-style: solid; + border-width: 1px; + border-radius: 4px; + border-color: var(--icons); + background-color: var(--theme-popup-bg); + transition: 100ms; + transition-property: color,border-color,background-color; + color: var(--icons); +} +@media (pointer: coarse) { + pre > .buttons button { + /* On mobile, make it easier to tap buttons. */ + padding: 0.3rem 1rem; + } + + .sidebar-resize-indicator { + /* Hide resize indicator on devices with limited accuracy */ + display: none; + } +} +pre > code { + display: block; + padding: 1rem; +} + +/* FIXME: ACE editors overlap their buttons because ACE does absolute + positioning within the code block which breaks padding. The only solution I + can think of is to move the padding to the outer pre tag (or insert a div + wrapper), but that would require fixing a whole bunch of CSS rules. +*/ +.hljs.ace_editor { + padding: 0rem 0rem; +} + +pre > .result { + margin-block-start: 10px; +} + +/* Search */ + +#searchresults a { + text-decoration: none; +} + +mark { + border-radius: 2px; + padding-block-start: 0; + padding-block-end: 1px; + padding-inline-start: 3px; + padding-inline-end: 3px; + margin-block-start: 0; + margin-block-end: -1px; + margin-inline-start: -3px; + margin-inline-end: -3px; + background-color: var(--search-mark-bg); + transition: background-color 300ms linear; + cursor: pointer; +} + +mark.fade-out { + background-color: rgba(0,0,0,0) !important; + cursor: auto; +} + +.searchbar-outer { + margin-inline-start: auto; + margin-inline-end: auto; + max-width: var(--content-max-width); +} + +#searchbar { + width: 100%; + margin-block-start: 5px; + margin-block-end: 0; + margin-inline-start: auto; + margin-inline-end: auto; + padding: 10px 16px; + transition: box-shadow 300ms ease-in-out; + border: 1px solid var(--searchbar-border-color); + border-radius: 3px; + background-color: var(--searchbar-bg); + color: var(--searchbar-fg); +} +#searchbar:focus, +#searchbar.active { + box-shadow: 0 0 3px var(--searchbar-shadow-color); +} + +.searchresults-header { + font-weight: bold; + font-size: 1em; + padding-block-start: 18px; + padding-block-end: 0; + padding-inline-start: 5px; + padding-inline-end: 0; + color: var(--searchresults-header-fg); +} + +.searchresults-outer { + margin-inline-start: auto; + margin-inline-end: auto; + max-width: var(--content-max-width); + border-block-end: 1px dashed var(--searchresults-border-color); +} + +ul#searchresults { + list-style: none; + padding-inline-start: 20px; +} +ul#searchresults li { + margin: 10px 0px; + padding: 2px; + border-radius: 2px; +} +ul#searchresults li.focus { + background-color: var(--searchresults-li-bg); +} +ul#searchresults span.teaser { + display: block; + clear: both; + margin-block-start: 5px; + margin-block-end: 0; + margin-inline-start: 20px; + margin-inline-end: 0; + font-size: 0.8em; +} +ul#searchresults span.teaser em { + font-weight: bold; + font-style: normal; +} + +/* Sidebar */ + +.sidebar { + position: fixed; + left: 0; + top: 0; + bottom: 0; + width: var(--sidebar-width); + font-size: 0.875em; + box-sizing: border-box; + -webkit-overflow-scrolling: touch; + overscroll-behavior-y: contain; + background-color: var(--sidebar-bg); + color: var(--sidebar-fg); +} +[dir=rtl] .sidebar { left: unset; right: 0; } +.sidebar-resizing { + -moz-user-select: none; + -webkit-user-select: none; + -ms-user-select: none; + user-select: none; +} +.no-js .sidebar, +.js:not(.sidebar-resizing) .sidebar { + transition: transform 0.3s; /* Animation: slide away */ +} +.sidebar code { + line-height: 2em; +} +.sidebar .sidebar-scrollbox { + overflow-y: auto; + position: absolute; + top: 0; + bottom: 0; + left: 0; + right: 0; + padding: 10px 10px; +} +.sidebar .sidebar-resize-handle { + position: absolute; + cursor: col-resize; + width: 0; + right: calc(var(--sidebar-resize-indicator-width) * -1); + top: 0; + bottom: 0; + display: flex; + align-items: center; +} + +.sidebar-resize-handle .sidebar-resize-indicator { + width: 100%; + height: 12px; + background-color: var(--icons); + margin-inline-start: var(--sidebar-resize-indicator-space); +} + +[dir=rtl] .sidebar .sidebar-resize-handle { + left: calc(var(--sidebar-resize-indicator-width) * -1); + right: unset; +} +.js .sidebar .sidebar-resize-handle { + cursor: col-resize; + width: calc(var(--sidebar-resize-indicator-width) - var(--sidebar-resize-indicator-space)); +} +/* sidebar-hidden */ +#sidebar-toggle-anchor:not(:checked) ~ .sidebar { + transform: translateX(calc(0px - var(--sidebar-width) - var(--sidebar-resize-indicator-width))); + z-index: -1; +} +[dir=rtl] #sidebar-toggle-anchor:not(:checked) ~ .sidebar { + transform: translateX(calc(var(--sidebar-width) + var(--sidebar-resize-indicator-width))); +} +.sidebar::-webkit-scrollbar { + background: var(--sidebar-bg); +} +.sidebar::-webkit-scrollbar-thumb { + background: var(--scrollbar); +} + +/* sidebar-visible */ +#sidebar-toggle-anchor:checked ~ .page-wrapper { + transform: translateX(calc(var(--sidebar-width) + var(--sidebar-resize-indicator-width))); +} +[dir=rtl] #sidebar-toggle-anchor:checked ~ .page-wrapper { + transform: translateX(calc(0px - var(--sidebar-width) - var(--sidebar-resize-indicator-width))); +} +@media only screen and (min-width: 620px) { + #sidebar-toggle-anchor:checked ~ .page-wrapper { + transform: none; + margin-inline-start: calc(var(--sidebar-width) + var(--sidebar-resize-indicator-width)); + } + [dir=rtl] #sidebar-toggle-anchor:checked ~ .page-wrapper { + transform: none; + } +} + +.chapter { + list-style: none outside none; + padding-inline-start: 0; + line-height: 2.2em; +} + +.chapter ol { + width: 100%; +} + +.chapter li { + display: flex; + color: var(--sidebar-non-existant); +} +.chapter li a { + display: block; + padding: 0; + text-decoration: none; + color: var(--sidebar-fg); +} + +.chapter li a:hover { + color: var(--sidebar-active); +} + +.chapter li a.active { + color: var(--sidebar-active); +} + +.chapter li > a.toggle { + cursor: pointer; + display: block; + margin-inline-start: auto; + padding: 0 10px; + user-select: none; + opacity: 0.68; +} + +.chapter li > a.toggle div { + transition: transform 0.5s; +} + +/* collapse the section */ +.chapter li:not(.expanded) + li > ol { + display: none; +} + +.chapter li.chapter-item { + line-height: 1.5em; + margin-block-start: 0.6em; +} + +.chapter li.expanded > a.toggle div { + transform: rotate(90deg); +} + +.spacer { + width: 100%; + height: 3px; + margin: 5px 0px; +} +.chapter .spacer { + background-color: var(--sidebar-spacer); +} + +@media (-moz-touch-enabled: 1), (pointer: coarse) { + .chapter li a { padding: 5px 0; } + .spacer { margin: 10px 0; } +} + +.section { + list-style: none outside none; + padding-inline-start: 20px; + line-height: 1.9em; +} + +/* Theme Menu Popup */ + +.theme-popup { + position: absolute; + left: 10px; + top: var(--menu-bar-height); + z-index: 1000; + border-radius: 4px; + font-size: 0.7em; + color: var(--fg); + background: var(--theme-popup-bg); + border: 1px solid var(--theme-popup-border); + margin: 0; + padding: 0; + list-style: none; + display: none; + /* Don't let the children's background extend past the rounded corners. */ + overflow: hidden; +} +[dir=rtl] .theme-popup { left: unset; right: 10px; } +.theme-popup .default { + color: var(--icons); +} +.theme-popup .theme { + width: 100%; + border: 0; + margin: 0; + padding: 2px 20px; + line-height: 25px; + white-space: nowrap; + text-align: start; + cursor: pointer; + color: inherit; + background: inherit; + font-size: inherit; +} +.theme-popup .theme:hover { + background-color: var(--theme-hover); +} + +.theme-selected::before { + display: inline-block; + content: "✓"; + margin-inline-start: -14px; + width: 14px; +} diff --git a/css/general.css b/css/general.css new file mode 100644 index 0000000..e7d20da --- /dev/null +++ b/css/general.css @@ -0,0 +1,234 @@ +/* Base styles and content styles */ + +@import 'variables.css'; + +:root { + /* Browser default font-size is 16px, this way 1 rem = 10px */ + font-size: 62.5%; + color-scheme: var(--color-scheme); +} + +html { + font-family: "Open Sans", sans-serif; + color: var(--fg); + background-color: var(--bg); + text-size-adjust: none; + -webkit-text-size-adjust: none; +} + +body { + margin: 0; + font-size: 1.6rem; + overflow-x: hidden; +} + +code { + font-family: var(--mono-font) !important; + font-size: var(--code-font-size); + direction: ltr !important; +} + +/* make long words/inline code not x overflow */ +main { + overflow-wrap: break-word; +} + +/* make wide tables scroll if they overflow */ +.table-wrapper { + overflow-x: auto; +} + +/* Don't change font size in headers. */ +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + font-size: unset; +} + +.left { float: left; } +.right { float: right; } +.boring { opacity: 0.6; } +.hide-boring .boring { display: none; } +.hidden { display: none !important; } + +h2, h3 { margin-block-start: 2.5em; } +h4, h5 { margin-block-start: 2em; } + +.header + .header h3, +.header + .header h4, +.header + .header h5 { + margin-block-start: 1em; +} + +h1:target::before, +h2:target::before, +h3:target::before, +h4:target::before, +h5:target::before, +h6:target::before { + display: inline-block; + content: "»"; + margin-inline-start: -30px; + width: 30px; +} + +/* This is broken on Safari as of version 14, but is fixed + in Safari Technology Preview 117 which I think will be Safari 14.2. + https://bugs.webkit.org/show_bug.cgi?id=218076 +*/ +:target { + /* Safari does not support logical properties */ + scroll-margin-top: calc(var(--menu-bar-height) + 0.5em); +} + +.page { + outline: 0; + padding: 0 var(--page-padding); + margin-block-start: calc(0px - var(--menu-bar-height)); /* Compensate for the #menu-bar-hover-placeholder */ +} +.page-wrapper { + box-sizing: border-box; + background-color: var(--bg); +} +.no-js .page-wrapper, +.js:not(.sidebar-resizing) .page-wrapper { + transition: margin-left 0.3s ease, transform 0.3s ease; /* Animation: slide away */ +} +[dir=rtl] .js:not(.sidebar-resizing) .page-wrapper { + transition: margin-right 0.3s ease, transform 0.3s ease; /* Animation: slide away */ +} + +.content { + overflow-y: auto; + padding: 0 5px 50px 5px; +} +.content main { + margin-inline-start: auto; + margin-inline-end: auto; + max-width: var(--content-max-width); +} +.content p { line-height: 1.45em; } +.content ol { line-height: 1.45em; } +.content ul { line-height: 1.45em; } +.content a { text-decoration: none; } +.content a:hover { text-decoration: underline; } +.content img, .content video { max-width: 100%; } +.content .header:link, +.content .header:visited { + color: var(--fg); +} +.content .header:link, +.content .header:visited:hover { + text-decoration: none; +} + +table { + margin: 0 auto; + border-collapse: collapse; +} +table td { + padding: 3px 20px; + border: 1px var(--table-border-color) solid; +} +table thead { + background: var(--table-header-bg); +} +table thead td { + font-weight: 700; + border: none; +} +table thead th { + padding: 3px 20px; +} +table thead tr { + border: 1px var(--table-header-bg) solid; +} +/* Alternate background colors for rows */ +table tbody tr:nth-child(2n) { + background: var(--table-alternate-bg); +} + + +blockquote { + margin: 20px 0; + padding: 0 20px; + color: var(--fg); + background-color: var(--quote-bg); + border-block-start: .1em solid var(--quote-border); + border-block-end: .1em solid var(--quote-border); +} + +.warning { + margin: 20px; + padding: 0 20px; + border-inline-start: 2px solid var(--warning-border); +} + +.warning:before { + position: absolute; + width: 3rem; + height: 3rem; + margin-inline-start: calc(-1.5rem - 21px); + content: "ⓘ"; + text-align: center; + background-color: var(--bg); + color: var(--warning-border); + font-weight: bold; + font-size: 2rem; +} + +blockquote .warning:before { + background-color: var(--quote-bg); +} + +kbd { + background-color: var(--table-border-color); + border-radius: 4px; + border: solid 1px var(--theme-popup-border); + box-shadow: inset 0 -1px 0 var(--theme-hover); + display: inline-block; + font-size: var(--code-font-size); + font-family: var(--mono-font); + line-height: 10px; + padding: 4px 5px; + vertical-align: middle; +} + +:not(.footnote-definition) + .footnote-definition, +.footnote-definition + :not(.footnote-definition) { + margin-block-start: 2em; +} +.footnote-definition { + font-size: 0.9em; + margin: 0.5em 0; +} +.footnote-definition p { + display: inline; +} + +.tooltiptext { + position: absolute; + visibility: hidden; + color: #fff; + background-color: #333; + transform: translateX(-50%); /* Center by moving tooltip 50% of its width left */ + left: -8px; /* Half of the width of the icon */ + top: -35px; + font-size: 0.8em; + text-align: center; + border-radius: 6px; + padding: 5px 8px; + margin: 5px; + z-index: 1000; +} +.tooltipped .tooltiptext { + visibility: visible; +} + +.chapter li.part-title { + color: var(--sidebar-fg); + margin: 5px 0px; + font-weight: bold; +} + +.result-no-output { + font-style: italic; +} diff --git a/css/print.css b/css/print.css new file mode 100644 index 0000000..80ec3a5 --- /dev/null +++ b/css/print.css @@ -0,0 +1,50 @@ + +#sidebar, +#menu-bar, +.nav-chapters, +.mobile-nav-chapters { + display: none; +} + +#page-wrapper.page-wrapper { + transform: none !important; + margin-inline-start: 0px; + overflow-y: initial; +} + +#content { + max-width: none; + margin: 0; + padding: 0; +} + +.page { + overflow-y: initial; +} + +code { + direction: ltr !important; +} + +pre > .buttons { + z-index: 2; +} + +a, a:visited, a:active, a:hover { + color: #4183c4; + text-decoration: none; +} + +h1, h2, h3, h4, h5, h6 { + page-break-inside: avoid; + page-break-after: avoid; +} + +pre, code { + page-break-inside: avoid; + white-space: pre-wrap; +} + +.fa { + display: none !important; +} diff --git a/css/variables.css b/css/variables.css new file mode 100644 index 0000000..0da55e8 --- /dev/null +++ b/css/variables.css @@ -0,0 +1,279 @@ + +/* Globals */ + +:root { + --sidebar-width: 300px; + --sidebar-resize-indicator-width: 8px; + --sidebar-resize-indicator-space: 2px; + --page-padding: 15px; + --content-max-width: 750px; + --menu-bar-height: 50px; + --mono-font: "Source Code Pro", Consolas, "Ubuntu Mono", Menlo, "DejaVu Sans Mono", monospace, monospace; + --code-font-size: 0.875em /* please adjust the ace font size accordingly in editor.js */ +} + +/* Themes */ + +.ayu { + --bg: hsl(210, 25%, 8%); + --fg: #c5c5c5; + + --sidebar-bg: #14191f; + --sidebar-fg: #c8c9db; + --sidebar-non-existant: #5c6773; + --sidebar-active: #ffb454; + --sidebar-spacer: #2d334f; + + --scrollbar: var(--sidebar-fg); + + --icons: #737480; + --icons-hover: #b7b9cc; + + --links: #0096cf; + + --inline-code-color: #ffb454; + + --theme-popup-bg: #14191f; + --theme-popup-border: #5c6773; + --theme-hover: #191f26; + + --quote-bg: hsl(226, 15%, 17%); + --quote-border: hsl(226, 15%, 22%); + + --warning-border: #ff8e00; + + --table-border-color: hsl(210, 25%, 13%); + --table-header-bg: hsl(210, 25%, 28%); + --table-alternate-bg: hsl(210, 25%, 11%); + + --searchbar-border-color: #848484; + --searchbar-bg: #424242; + --searchbar-fg: #fff; + --searchbar-shadow-color: #d4c89f; + --searchresults-header-fg: #666; + --searchresults-border-color: #888; + --searchresults-li-bg: #252932; + --search-mark-bg: #e3b171; + + --color-scheme: dark; +} + +.coal { + --bg: hsl(200, 7%, 8%); + --fg: #98a3ad; + + --sidebar-bg: #292c2f; + --sidebar-fg: #a1adb8; + --sidebar-non-existant: #505254; + --sidebar-active: #3473ad; + --sidebar-spacer: #393939; + + --scrollbar: var(--sidebar-fg); + + --icons: #43484d; + --icons-hover: #b3c0cc; + + --links: #2b79a2; + + --inline-code-color: #c5c8c6; + + --theme-popup-bg: #141617; + --theme-popup-border: #43484d; + --theme-hover: #1f2124; + + --quote-bg: hsl(234, 21%, 18%); + --quote-border: hsl(234, 21%, 23%); + + --warning-border: #ff8e00; + + --table-border-color: hsl(200, 7%, 13%); + --table-header-bg: hsl(200, 7%, 28%); + --table-alternate-bg: hsl(200, 7%, 11%); + + --searchbar-border-color: #aaa; + --searchbar-bg: #b7b7b7; + --searchbar-fg: #000; + --searchbar-shadow-color: #aaa; + --searchresults-header-fg: #666; + --searchresults-border-color: #98a3ad; + --searchresults-li-bg: #2b2b2f; + --search-mark-bg: #355c7d; + + --color-scheme: dark; +} + +.light { + --bg: hsl(0, 0%, 100%); + --fg: hsl(0, 0%, 0%); + + --sidebar-bg: #fafafa; + --sidebar-fg: hsl(0, 0%, 0%); + --sidebar-non-existant: #aaaaaa; + --sidebar-active: #1f1fff; + --sidebar-spacer: #f4f4f4; + + --scrollbar: #8F8F8F; + + --icons: #747474; + --icons-hover: #000000; + + --links: #20609f; + + --inline-code-color: #301900; + + --theme-popup-bg: #fafafa; + --theme-popup-border: #cccccc; + --theme-hover: #e6e6e6; + + --quote-bg: hsl(197, 37%, 96%); + --quote-border: hsl(197, 37%, 91%); + + --warning-border: #ff8e00; + + --table-border-color: hsl(0, 0%, 95%); + --table-header-bg: hsl(0, 0%, 80%); + --table-alternate-bg: hsl(0, 0%, 97%); + + --searchbar-border-color: #aaa; + --searchbar-bg: #fafafa; + --searchbar-fg: #000; + --searchbar-shadow-color: #aaa; + --searchresults-header-fg: #666; + --searchresults-border-color: #888; + --searchresults-li-bg: #e4f2fe; + --search-mark-bg: #a2cff5; + + --color-scheme: light; +} + +.navy { + --bg: hsl(226, 23%, 11%); + --fg: #bcbdd0; + + --sidebar-bg: #282d3f; + --sidebar-fg: #c8c9db; + --sidebar-non-existant: #505274; + --sidebar-active: #2b79a2; + --sidebar-spacer: #2d334f; + + --scrollbar: var(--sidebar-fg); + + --icons: #737480; + --icons-hover: #b7b9cc; + + --links: #2b79a2; + + --inline-code-color: #c5c8c6; + + --theme-popup-bg: #161923; + --theme-popup-border: #737480; + --theme-hover: #282e40; + + --quote-bg: hsl(226, 15%, 17%); + --quote-border: hsl(226, 15%, 22%); + + --warning-border: #ff8e00; + + --table-border-color: hsl(226, 23%, 16%); + --table-header-bg: hsl(226, 23%, 31%); + --table-alternate-bg: hsl(226, 23%, 14%); + + --searchbar-border-color: #aaa; + --searchbar-bg: #aeaec6; + --searchbar-fg: #000; + --searchbar-shadow-color: #aaa; + --searchresults-header-fg: #5f5f71; + --searchresults-border-color: #5c5c68; + --searchresults-li-bg: #242430; + --search-mark-bg: #a2cff5; + + --color-scheme: dark; +} + +.rust { + --bg: hsl(60, 9%, 87%); + --fg: #262625; + + --sidebar-bg: #3b2e2a; + --sidebar-fg: #c8c9db; + --sidebar-non-existant: #505254; + --sidebar-active: #e69f67; + --sidebar-spacer: #45373a; + + --scrollbar: var(--sidebar-fg); + + --icons: #737480; + --icons-hover: #262625; + + --links: #2b79a2; + + --inline-code-color: #6e6b5e; + + --theme-popup-bg: #e1e1db; + --theme-popup-border: #b38f6b; + --theme-hover: #99908a; + + --quote-bg: hsl(60, 5%, 75%); + --quote-border: hsl(60, 5%, 70%); + + --warning-border: #ff8e00; + + --table-border-color: hsl(60, 9%, 82%); + --table-header-bg: #b3a497; + --table-alternate-bg: hsl(60, 9%, 84%); + + --searchbar-border-color: #aaa; + --searchbar-bg: #fafafa; + --searchbar-fg: #000; + --searchbar-shadow-color: #aaa; + --searchresults-header-fg: #666; + --searchresults-border-color: #888; + --searchresults-li-bg: #dec2a2; + --search-mark-bg: #e69f67; + + --color-scheme: light; +} + +@media (prefers-color-scheme: dark) { + .light.no-js { + --bg: hsl(200, 7%, 8%); + --fg: #98a3ad; + + --sidebar-bg: #292c2f; + --sidebar-fg: #a1adb8; + --sidebar-non-existant: #505254; + --sidebar-active: #3473ad; + --sidebar-spacer: #393939; + + --scrollbar: var(--sidebar-fg); + + --icons: #43484d; + --icons-hover: #b3c0cc; + + --links: #2b79a2; + + --inline-code-color: #c5c8c6; + + --theme-popup-bg: #141617; + --theme-popup-border: #43484d; + --theme-hover: #1f2124; + + --quote-bg: hsl(234, 21%, 18%); + --quote-border: hsl(234, 21%, 23%); + + --warning-border: #ff8e00; + + --table-border-color: hsl(200, 7%, 13%); + --table-header-bg: hsl(200, 7%, 28%); + --table-alternate-bg: hsl(200, 7%, 11%); + + --searchbar-border-color: #aaa; + --searchbar-bg: #b7b7b7; + --searchbar-fg: #000; + --searchbar-shadow-color: #aaa; + --searchresults-header-fg: #666; + --searchresults-border-color: #98a3ad; + --searchresults-li-bg: #2b2b2f; + --search-mark-bg: #355c7d; + } +} diff --git a/elasticlunr.min.js b/elasticlunr.min.js new file mode 100644 index 0000000..94b20dd --- /dev/null +++ b/elasticlunr.min.js @@ -0,0 +1,10 @@ +/** + * elasticlunr - http://weixsong.github.io + * Lightweight full-text search engine in Javascript for browser search and offline search. - 0.9.5 + * + * Copyright (C) 2017 Oliver Nightingale + * Copyright (C) 2017 Wei Song + * MIT Licensed + * @license + */ +!function(){function e(e){if(null===e||"object"!=typeof e)return e;var t=e.constructor();for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n]);return t}var t=function(e){var n=new t.Index;return n.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),e&&e.call(n,n),n};t.version="0.9.5",lunr=t,t.utils={},t.utils.warn=function(e){return function(t){e.console&&console.warn&&console.warn(t)}}(this),t.utils.toString=function(e){return void 0===e||null===e?"":e.toString()},t.EventEmitter=function(){this.events={}},t.EventEmitter.prototype.addListener=function(){var e=Array.prototype.slice.call(arguments),t=e.pop(),n=e;if("function"!=typeof t)throw new TypeError("last argument must be a function");n.forEach(function(e){this.hasHandler(e)||(this.events[e]=[]),this.events[e].push(t)},this)},t.EventEmitter.prototype.removeListener=function(e,t){if(this.hasHandler(e)){var n=this.events[e].indexOf(t);-1!==n&&(this.events[e].splice(n,1),0==this.events[e].length&&delete this.events[e])}},t.EventEmitter.prototype.emit=function(e){if(this.hasHandler(e)){var t=Array.prototype.slice.call(arguments,1);this.events[e].forEach(function(e){e.apply(void 0,t)},this)}},t.EventEmitter.prototype.hasHandler=function(e){return e in this.events},t.tokenizer=function(e){if(!arguments.length||null===e||void 0===e)return[];if(Array.isArray(e)){var n=e.filter(function(e){return null===e||void 0===e?!1:!0});n=n.map(function(e){return t.utils.toString(e).toLowerCase()});var i=[];return n.forEach(function(e){var n=e.split(t.tokenizer.seperator);i=i.concat(n)},this),i}return e.toString().trim().toLowerCase().split(t.tokenizer.seperator)},t.tokenizer.defaultSeperator=/[\s\-]+/,t.tokenizer.seperator=t.tokenizer.defaultSeperator,t.tokenizer.setSeperator=function(e){null!==e&&void 0!==e&&"object"==typeof e&&(t.tokenizer.seperator=e)},t.tokenizer.resetSeperator=function(){t.tokenizer.seperator=t.tokenizer.defaultSeperator},t.tokenizer.getSeperator=function(){return t.tokenizer.seperator},t.Pipeline=function(){this._queue=[]},t.Pipeline.registeredFunctions={},t.Pipeline.registerFunction=function(e,n){n in t.Pipeline.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+n),e.label=n,t.Pipeline.registeredFunctions[n]=e},t.Pipeline.getRegisteredFunction=function(e){return e in t.Pipeline.registeredFunctions!=!0?null:t.Pipeline.registeredFunctions[e]},t.Pipeline.warnIfFunctionNotRegistered=function(e){var n=e.label&&e.label in this.registeredFunctions;n||t.utils.warn("Function is not registered with pipeline. This may cause problems when serialising the index.\n",e)},t.Pipeline.load=function(e){var n=new t.Pipeline;return e.forEach(function(e){var i=t.Pipeline.getRegisteredFunction(e);if(!i)throw new Error("Cannot load un-registered function: "+e);n.add(i)}),n},t.Pipeline.prototype.add=function(){var e=Array.prototype.slice.call(arguments);e.forEach(function(e){t.Pipeline.warnIfFunctionNotRegistered(e),this._queue.push(e)},this)},t.Pipeline.prototype.after=function(e,n){t.Pipeline.warnIfFunctionNotRegistered(n);var i=this._queue.indexOf(e);if(-1===i)throw new Error("Cannot find existingFn");this._queue.splice(i+1,0,n)},t.Pipeline.prototype.before=function(e,n){t.Pipeline.warnIfFunctionNotRegistered(n);var i=this._queue.indexOf(e);if(-1===i)throw new Error("Cannot find existingFn");this._queue.splice(i,0,n)},t.Pipeline.prototype.remove=function(e){var t=this._queue.indexOf(e);-1!==t&&this._queue.splice(t,1)},t.Pipeline.prototype.run=function(e){for(var t=[],n=e.length,i=this._queue.length,o=0;n>o;o++){for(var r=e[o],s=0;i>s&&(r=this._queue[s](r,o,e),void 0!==r&&null!==r);s++);void 0!==r&&null!==r&&t.push(r)}return t},t.Pipeline.prototype.reset=function(){this._queue=[]},t.Pipeline.prototype.get=function(){return this._queue},t.Pipeline.prototype.toJSON=function(){return this._queue.map(function(e){return t.Pipeline.warnIfFunctionNotRegistered(e),e.label})},t.Index=function(){this._fields=[],this._ref="id",this.pipeline=new t.Pipeline,this.documentStore=new t.DocumentStore,this.index={},this.eventEmitter=new t.EventEmitter,this._idfCache={},this.on("add","remove","update",function(){this._idfCache={}}.bind(this))},t.Index.prototype.on=function(){var e=Array.prototype.slice.call(arguments);return this.eventEmitter.addListener.apply(this.eventEmitter,e)},t.Index.prototype.off=function(e,t){return this.eventEmitter.removeListener(e,t)},t.Index.load=function(e){e.version!==t.version&&t.utils.warn("version mismatch: current "+t.version+" importing "+e.version);var n=new this;n._fields=e.fields,n._ref=e.ref,n.documentStore=t.DocumentStore.load(e.documentStore),n.pipeline=t.Pipeline.load(e.pipeline),n.index={};for(var i in e.index)n.index[i]=t.InvertedIndex.load(e.index[i]);return n},t.Index.prototype.addField=function(e){return this._fields.push(e),this.index[e]=new t.InvertedIndex,this},t.Index.prototype.setRef=function(e){return this._ref=e,this},t.Index.prototype.saveDocument=function(e){return this.documentStore=new t.DocumentStore(e),this},t.Index.prototype.addDoc=function(e,n){if(e){var n=void 0===n?!0:n,i=e[this._ref];this.documentStore.addDoc(i,e),this._fields.forEach(function(n){var o=this.pipeline.run(t.tokenizer(e[n]));this.documentStore.addFieldLength(i,n,o.length);var r={};o.forEach(function(e){e in r?r[e]+=1:r[e]=1},this);for(var s in r){var u=r[s];u=Math.sqrt(u),this.index[n].addToken(s,{ref:i,tf:u})}},this),n&&this.eventEmitter.emit("add",e,this)}},t.Index.prototype.removeDocByRef=function(e){if(e&&this.documentStore.isDocStored()!==!1&&this.documentStore.hasDoc(e)){var t=this.documentStore.getDoc(e);this.removeDoc(t,!1)}},t.Index.prototype.removeDoc=function(e,n){if(e){var n=void 0===n?!0:n,i=e[this._ref];this.documentStore.hasDoc(i)&&(this.documentStore.removeDoc(i),this._fields.forEach(function(n){var o=this.pipeline.run(t.tokenizer(e[n]));o.forEach(function(e){this.index[n].removeToken(e,i)},this)},this),n&&this.eventEmitter.emit("remove",e,this))}},t.Index.prototype.updateDoc=function(e,t){var t=void 0===t?!0:t;this.removeDocByRef(e[this._ref],!1),this.addDoc(e,!1),t&&this.eventEmitter.emit("update",e,this)},t.Index.prototype.idf=function(e,t){var n="@"+t+"/"+e;if(Object.prototype.hasOwnProperty.call(this._idfCache,n))return this._idfCache[n];var i=this.index[t].getDocFreq(e),o=1+Math.log(this.documentStore.length/(i+1));return this._idfCache[n]=o,o},t.Index.prototype.getFields=function(){return this._fields.slice()},t.Index.prototype.search=function(e,n){if(!e)return[];e="string"==typeof e?{any:e}:JSON.parse(JSON.stringify(e));var i=null;null!=n&&(i=JSON.stringify(n));for(var o=new t.Configuration(i,this.getFields()).get(),r={},s=Object.keys(e),u=0;u0&&t.push(e);for(var i in n)"docs"!==i&&"df"!==i&&this.expandToken(e+i,t,n[i]);return t},t.InvertedIndex.prototype.toJSON=function(){return{root:this.root}},t.Configuration=function(e,n){var e=e||"";if(void 0==n||null==n)throw new Error("fields should not be null");this.config={};var i;try{i=JSON.parse(e),this.buildUserConfig(i,n)}catch(o){t.utils.warn("user configuration parse failed, will use default configuration"),this.buildDefaultConfig(n)}},t.Configuration.prototype.buildDefaultConfig=function(e){this.reset(),e.forEach(function(e){this.config[e]={boost:1,bool:"OR",expand:!1}},this)},t.Configuration.prototype.buildUserConfig=function(e,n){var i="OR",o=!1;if(this.reset(),"bool"in e&&(i=e.bool||i),"expand"in e&&(o=e.expand||o),"fields"in e)for(var r in e.fields)if(n.indexOf(r)>-1){var s=e.fields[r],u=o;void 0!=s.expand&&(u=s.expand),this.config[r]={boost:s.boost||0===s.boost?s.boost:1,bool:s.bool||i,expand:u}}else t.utils.warn("field name in user configuration not found in index instance fields");else this.addAllFields2UserConfig(i,o,n)},t.Configuration.prototype.addAllFields2UserConfig=function(e,t,n){n.forEach(function(n){this.config[n]={boost:1,bool:e,expand:t}},this)},t.Configuration.prototype.get=function(){return this.config},t.Configuration.prototype.reset=function(){this.config={}},lunr.SortedSet=function(){this.length=0,this.elements=[]},lunr.SortedSet.load=function(e){var t=new this;return t.elements=e,t.length=e.length,t},lunr.SortedSet.prototype.add=function(){var e,t;for(e=0;e1;){if(r===e)return o;e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o]}return r===e?o:-1},lunr.SortedSet.prototype.locationFor=function(e){for(var t=0,n=this.elements.length,i=n-t,o=t+Math.floor(i/2),r=this.elements[o];i>1;)e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o];return r>e?o:e>r?o+1:void 0},lunr.SortedSet.prototype.intersect=function(e){for(var t=new lunr.SortedSet,n=0,i=0,o=this.length,r=e.length,s=this.elements,u=e.elements;;){if(n>o-1||i>r-1)break;s[n]!==u[i]?s[n]u[i]&&i++:(t.add(s[n]),n++,i++)}return t},lunr.SortedSet.prototype.clone=function(){var e=new lunr.SortedSet;return e.elements=this.toArray(),e.length=e.elements.length,e},lunr.SortedSet.prototype.union=function(e){var t,n,i;this.length>=e.length?(t=this,n=e):(t=e,n=this),i=t.clone();for(var o=0,r=n.toArray();o + + + + diff --git a/fonts/OPEN-SANS-LICENSE.txt b/fonts/OPEN-SANS-LICENSE.txt new file mode 100644 index 0000000..d645695 --- /dev/null +++ b/fonts/OPEN-SANS-LICENSE.txt @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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All Rights Reserved. Source is a trademark of Adobe Systems Incorporated in the United States and/or other countries. + +This Font Software is licensed under the SIL Open Font License, Version 1.1. +This license is copied below, and is also available with a FAQ at: +http://scripts.sil.org/OFL + + +----------------------------------------------------------- +SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007 +----------------------------------------------------------- + +PREAMBLE +The goals of the Open Font License (OFL) are to stimulate worldwide +development of collaborative font projects, to support the font creation +efforts of academic and linguistic communities, and to provide a free and +open framework in which fonts may be shared and improved in partnership +with others. + +The OFL allows the licensed fonts to be used, studied, modified and +redistributed freely as long as they are not sold by themselves. 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This may +include source files, build scripts and documentation. + +"Reserved Font Name" refers to any names specified as such after the +copyright statement(s). + +"Original Version" refers to the collection of Font Software components as +distributed by the Copyright Holder(s). + +"Modified Version" refers to any derivative made by adding to, deleting, +or substituting -- in part or in whole -- any of the components of the +Original Version, by changing formats or by porting the Font Software to a +new environment. + +"Author" refers to any designer, engineer, programmer, technical +writer or other person who contributed to the Font Software. + +PERMISSION & CONDITIONS +Permission is hereby granted, free of charge, to any person obtaining +a copy of the Font Software, to use, study, copy, merge, embed, modify, +redistribute, and sell modified and unmodified copies of the Font +Software, subject to the following conditions: + +1) Neither the Font Software nor any of its individual components, +in Original or Modified Versions, may be sold by itself. + +2) Original or Modified Versions of the Font Software may be bundled, +redistributed and/or sold with any software, provided that each copy +contains the above copyright notice and this license. These can be +included either as stand-alone text files, human-readable headers or +in the appropriate machine-readable metadata fields within text or +binary files as long as those fields can be easily viewed by the user. + +3) No Modified Version of the Font Software may use the Reserved Font +Name(s) unless explicit written permission is granted by the corresponding +Copyright Holder. This restriction only applies to the primary font name as +presented to the users. + +4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font +Software shall not be used to promote, endorse or advertise any +Modified Version, except to acknowledge the contribution(s) of the +Copyright Holder(s) and the Author(s) or with their explicit written +permission. + +5) The Font Software, modified or unmodified, in part or in whole, +must be distributed entirely under this license, and must not be +distributed under any other license. The requirement for fonts to +remain under this license does not apply to any document created +using the Font Software. + +TERMINATION +This license becomes null and void if any of the above conditions are +not met. + +DISCLAIMER +THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT +OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE +COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL +DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM +OTHER DEALINGS IN THE FONT SOFTWARE. diff --git a/fonts/fonts.css b/fonts/fonts.css new file mode 100644 index 0000000..858efa5 --- /dev/null +++ b/fonts/fonts.css @@ -0,0 +1,100 @@ +/* Open Sans is licensed under the Apache License, Version 2.0. See http://www.apache.org/licenses/LICENSE-2.0 */ +/* Source Code Pro is under the Open Font License. See https://scripts.sil.org/cms/scripts/page.php?site_id=nrsi&id=OFL */ + +/* open-sans-300 - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */ +@font-face { + font-family: 'Open Sans'; + font-style: normal; + font-weight: 300; + src: local('Open Sans Light'), local('OpenSans-Light'), + url('open-sans-v17-all-charsets-300.woff2') format('woff2'); +} + +/* open-sans-300italic - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */ +@font-face { + font-family: 'Open Sans'; + font-style: italic; + font-weight: 300; + src: local('Open Sans Light Italic'), local('OpenSans-LightItalic'), + url('open-sans-v17-all-charsets-300italic.woff2') format('woff2'); +} + +/* open-sans-regular - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */ +@font-face { + font-family: 'Open Sans'; + font-style: normal; + font-weight: 400; + src: local('Open Sans Regular'), local('OpenSans-Regular'), + url('open-sans-v17-all-charsets-regular.woff2') format('woff2'); +} + +/* open-sans-italic - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */ +@font-face { + font-family: 'Open Sans'; + font-style: italic; + font-weight: 400; + src: local('Open Sans Italic'), local('OpenSans-Italic'), + url('open-sans-v17-all-charsets-italic.woff2') format('woff2'); +} + +/* open-sans-600 - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */ +@font-face { + font-family: 'Open Sans'; + font-style: normal; + font-weight: 600; + src: local('Open Sans SemiBold'), local('OpenSans-SemiBold'), + url('open-sans-v17-all-charsets-600.woff2') format('woff2'); +} + +/* open-sans-600italic - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */ +@font-face { + font-family: 'Open Sans'; + font-style: italic; + font-weight: 600; + src: local('Open Sans SemiBold Italic'), local('OpenSans-SemiBoldItalic'), + url('open-sans-v17-all-charsets-600italic.woff2') format('woff2'); +} + +/* open-sans-700 - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */ +@font-face { + font-family: 'Open Sans'; + font-style: normal; + font-weight: 700; + src: local('Open Sans Bold'), local('OpenSans-Bold'), + url('open-sans-v17-all-charsets-700.woff2') format('woff2'); +} + +/* open-sans-700italic - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */ +@font-face { + font-family: 'Open Sans'; + font-style: italic; + font-weight: 700; + src: local('Open Sans Bold Italic'), local('OpenSans-BoldItalic'), + url('open-sans-v17-all-charsets-700italic.woff2') format('woff2'); +} + +/* open-sans-800 - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */ +@font-face { + font-family: 'Open Sans'; + font-style: normal; + font-weight: 800; + src: local('Open Sans ExtraBold'), local('OpenSans-ExtraBold'), + url('open-sans-v17-all-charsets-800.woff2') format('woff2'); +} + +/* open-sans-800italic - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */ 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@@ -0,0 +1,250 @@ + + + + + + Home - Notes @ ETH Zürich + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

Notes taken @ ETH Zurich

+

Introduction

+

Here I list all courses I took at ETH Zurich and provide a brief overview of the course content. The clickable links will lead you to the respective course notes.

+

Courses are organized by semester and year. The course notes are organized by lecture.

+

22HS

+
    +
  • Computational Biology
    • +
  • Data Mining I
    • +
  • Information Systems for Engineers
    • +
  • Computational Systems Biology
    • +
+

23FS + HS

+ +

No courses (except for seminar) taken in 23HS since I was doing an internship at Roche.

+

24FS

+
    +
  • Biofluiddynamics
    • +
  • Synthetic Biology I
    • +
+ +
+ + +
+
+ + + +
+ + + + + + + + + + + + + + + + + + + + +
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f,p,w,m,b,E,_,A,I,B,N;if(this.primaryTextColor=this.primaryTextColor||(this.darkMode?"#eee":"#333"),this.secondaryColor=this.secondaryColor||xn(this.primaryColor,{h:-120}),this.tertiaryColor=this.tertiaryColor||xn(this.primaryColor,{h:180,l:5}),this.primaryBorderColor=this.primaryBorderColor||lg(this.primaryColor,this.darkMode),this.secondaryBorderColor=this.secondaryBorderColor||lg(this.secondaryColor,this.darkMode),this.tertiaryBorderColor=this.tertiaryBorderColor||lg(this.tertiaryColor,this.darkMode),this.noteBorderColor=this.noteBorderColor||lg(this.noteBkgColor,this.darkMode),this.noteBkgColor=this.noteBkgColor||"#fff5ad",this.noteTextColor=this.noteTextColor||"#333",this.secondaryTextColor=this.secondaryTextColor||Di(this.secondaryColor),this.tertiaryTextColor=this.tertiaryTextColor||Di(this.tertiaryColor),this.lineColor=this.lineColor||Di(this.background),this.arrowheadColor=this.arrowheadColor||Di(this.background),this.textColor=this.textColor||this.primaryTextColor,this.border2=this.border2||this.tertiaryBorderColor,this.nodeBkg=this.nodeBkg||this.primaryColor,this.mainBkg=this.mainBkg||this.primaryColor,this.nodeBorder=this.nodeBorder||this.primaryBorderColor,this.clusterBkg=this.clusterBkg||this.tertiaryColor,this.clusterBorder=this.clusterBorder||this.tertiaryBorderColor,this.defaultLinkColor=this.defaultLinkColor||this.lineColor,this.titleColor=this.titleColor||this.tertiaryTextColor,this.edgeLabelBackground=this.edgeLabelBackground||(this.darkMode?$s(this.secondaryColor,30):this.secondaryColor),this.nodeTextColor=this.nodeTextColor||this.primaryTextColor,this.actorBorder=this.actorBorder||this.primaryBorderColor,this.actorBkg=this.actorBkg||this.mainBkg,this.actorTextColor=this.actorTextColor||this.primaryTextColor,this.actorLineColor=this.actorLineColor||"grey",this.labelBoxBkgColor=this.labelBoxBkgColor||this.actorBkg,this.signalColor=this.signalColor||this.textColor,this.signalTextColor=this.signalTextColor||this.textColor,this.labelBoxBorderColor=this.labelBoxBorderColor||this.actorBorder,this.labelTextColor=this.labelTextColor||this.actorTextColor,this.loopTextColor=this.loopTextColor||this.actorTextColor,this.activationBorderColor=this.activationBorderColor||$s(this.secondaryColor,10),this.activationBkgColor=this.activationBkgColor||this.secondaryColor,this.sequenceNumberColor=this.sequenceNumberColor||Di(this.lineColor),this.sectionBkgColor=this.sectionBkgColor||this.tertiaryColor,this.altSectionBkgColor=this.altSectionBkgColor||"white",this.sectionBkgColor=this.sectionBkgColor||this.secondaryColor,this.sectionBkgColor2=this.sectionBkgColor2||this.primaryColor,this.excludeBkgColor=this.excludeBkgColor||"#eeeeee",this.taskBorderColor=this.taskBorderColor||this.primaryBorderColor,this.taskBkgColor=this.taskBkgColor||this.primaryColor,this.activeTaskBorderColor=this.activeTaskBorderColor||this.primaryColor,this.activeTaskBkgColor=this.activeTaskBkgColor||bs(this.primaryColor,23),this.gridColor=this.gridColor||"lightgrey",this.doneTaskBkgColor=this.doneTaskBkgColor||"lightgrey",this.doneTaskBorderColor=this.doneTaskBorderColor||"grey",this.critBorderColor=this.critBorderColor||"#ff8888",this.critBkgColor=this.critBkgColor||"red",this.todayLineColor=this.todayLineColor||"red",this.taskTextColor=this.taskTextColor||this.textColor,this.taskTextOutsideColor=this.taskTextOutsideColor||this.textColor,this.taskTextLightColor=this.taskTextLightColor||this.textColor,this.taskTextColor=this.taskTextColor||this.primaryTextColor,this.taskTextDarkColor=this.taskTextDarkColor||this.textColor,this.taskTextClickableColor=this.taskTextClickableColor||"#003163",this.personBorder=this.personBorder||this.primaryBorderColor,this.personBkg=this.personBkg||this.mainBkg,this.transitionColor=this.transitionColor||this.lineColor,this.transitionLabelColor=this.transitionLabelColor||this.textColor,this.stateLabelColor=this.stateLabelColor||this.stateBkg||this.primaryTextColor,this.stateBkg=this.stateBkg||this.mainBkg,this.labelBackgroundColor=this.labelBackgroundColor||this.stateBkg,this.compositeBackground=this.compositeBackground||this.background||this.tertiaryColor,this.altBackground=this.altBackground||this.tertiaryColor,this.compositeTitleBackground=this.compositeTitleBackground||this.mainBkg,this.compositeBorder=this.compositeBorder||this.nodeBorder,this.innerEndBackground=this.nodeBorder,this.errorBkgColor=this.errorBkgColor||this.tertiaryColor,this.errorTextColor=this.errorTextColor||this.tertiaryTextColor,this.transitionColor=this.transitionColor||this.lineColor,this.specialStateColor=this.lineColor,this.cScale0=this.cScale0||this.primaryColor,this.cScale1=this.cScale1||this.secondaryColor,this.cScale2=this.cScale2||this.tertiaryColor,this.cScale3=this.cScale3||xn(this.primaryColor,{h:30}),this.cScale4=this.cScale4||xn(this.primaryColor,{h:60}),this.cScale5=this.cScale5||xn(this.primaryColor,{h:90}),this.cScale6=this.cScale6||xn(this.primaryColor,{h:120}),this.cScale7=this.cScale7||xn(this.primaryColor,{h:150}),this.cScale8=this.cScale8||xn(this.primaryColor,{h:210,l:150}),this.cScale9=this.cScale9||xn(this.primaryColor,{h:270}),this.cScale10=this.cScale10||xn(this.primaryColor,{h:300}),this.cScale11=this.cScale11||xn(this.primaryColor,{h:330}),this.darkMode)for(let R=0;R{this[p]=a[p]}),this.updateColors(),f.forEach(p=>{this[p]=a[p]})}};const dCe=i=>{const a=new fCe;return a.calculate(i),a};let gCe=class{constructor(){this.background="#333",this.primaryColor="#1f2020",this.secondaryColor=bs(this.primaryColor,16),this.tertiaryColor=xn(this.primaryColor,{h:-160}),this.primaryBorderColor=Di(this.background),this.secondaryBorderColor=lg(this.secondaryColor,this.darkMode),this.tertiaryBorderColor=lg(this.tertiaryColor,this.darkMode),this.primaryTextColor=Di(this.primaryColor),this.secondaryTextColor=Di(this.secondaryColor),this.tertiaryTextColor=Di(this.tertiaryColor),this.lineColor=Di(this.background),this.textColor=Di(this.background),this.mainBkg="#1f2020",this.secondBkg="calculated",this.mainContrastColor="lightgrey",this.darkTextColor=bs(Di("#323D47"),10),this.lineColor="calculated",this.border1="#81B1DB",this.border2=FA(255,255,255,.25),this.arrowheadColor="calculated",this.fontFamily='"trebuchet ms", verdana, arial, sans-serif',this.fontSize="16px",this.labelBackground="#181818",this.textColor="#ccc",this.THEME_COLOR_LIMIT=12,this.nodeBkg="calculated",this.nodeBorder="calculated",this.clusterBkg="calculated",this.clusterBorder="calculated",this.defaultLinkColor="calculated",this.titleColor="#F9FFFE",this.edgeLabelBackground="calculated",this.actorBorder="calculated",this.actorBkg="calculated",this.actorTextColor="calculated",this.actorLineColor="calculated",this.signalColor="calculated",this.signalTextColor="calculated",this.labelBoxBkgColor="calculated",this.labelBoxBorderColor="calculated",this.labelTextColor="calculated",this.loopTextColor="calculated",this.noteBorderColor="calculated",this.noteBkgColor="#fff5ad",this.noteTextColor="calculated",this.activationBorderColor="calculated",this.activationBkgColor="calculated",this.sequenceNumberColor="black",this.sectionBkgColor=$s("#EAE8D9",30),this.altSectionBkgColor="calculated",this.sectionBkgColor2="#EAE8D9",this.excludeBkgColor=$s(this.sectionBkgColor,10),this.taskBorderColor=FA(255,255,255,70),this.taskBkgColor="calculated",this.taskTextColor="calculated",this.taskTextLightColor="calculated",this.taskTextOutsideColor="calculated",this.taskTextClickableColor="#003163",this.activeTaskBorderColor=FA(255,255,255,50),this.activeTaskBkgColor="#81B1DB",this.gridColor="calculated",this.doneTaskBkgColor="calculated",this.doneTaskBorderColor="grey",this.critBorderColor="#E83737",this.critBkgColor="#E83737",this.taskTextDarkColor="calculated",this.todayLineColor="#DB5757",this.personBorder=this.primaryBorderColor,this.personBkg=this.mainBkg,this.labelColor="calculated",this.errorBkgColor="#a44141",this.errorTextColor="#ddd"}updateColors(){var a,f,p,w,m,b,E,_,A,I,B;this.secondBkg=bs(this.mainBkg,16),this.lineColor=this.mainContrastColor,this.arrowheadColor=this.mainContrastColor,this.nodeBkg=this.mainBkg,this.nodeBorder=this.border1,this.clusterBkg=this.secondBkg,this.clusterBorder=this.border2,this.defaultLinkColor=this.lineColor,this.edgeLabelBackground=bs(this.labelBackground,25),this.actorBorder=this.border1,this.actorBkg=this.mainBkg,this.actorTextColor=this.mainContrastColor,this.actorLineColor=this.mainContrastColor,this.signalColor=this.mainContrastColor,this.signalTextColor=this.mainContrastColor,this.labelBoxBkgColor=this.actorBkg,this.labelBoxBorderColor=this.actorBorder,this.labelTextColor=this.mainContrastColor,this.loopTextColor=this.mainContrastColor,this.noteBorderColor=this.secondaryBorderColor,this.noteBkgColor=this.secondBkg,this.noteTextColor=this.secondaryTextColor,this.activationBorderColor=this.border1,this.activationBkgColor=this.secondBkg,this.altSectionBkgColor=this.background,this.taskBkgColor=bs(this.mainBkg,23),this.taskTextColor=this.darkTextColor,this.taskTextLightColor=this.mainContrastColor,this.taskTextOutsideColor=this.taskTextLightColor,this.gridColor=this.mainContrastColor,this.doneTaskBkgColor=this.mainContrastColor,this.taskTextDarkColor=this.darkTextColor,this.transitionColor=this.transitionColor||this.lineColor,this.transitionLabelColor=this.transitionLabelColor||this.textColor,this.stateLabelColor=this.stateLabelColor||this.stateBkg||this.primaryTextColor,this.stateBkg=this.stateBkg||this.mainBkg,this.labelBackgroundColor=this.labelBackgroundColor||this.stateBkg,this.compositeBackground=this.compositeBackground||this.background||this.tertiaryColor,this.altBackground=this.altBackground||"#555",this.compositeTitleBackground=this.compositeTitleBackground||this.mainBkg,this.compositeBorder=this.compositeBorder||this.nodeBorder,this.innerEndBackground=this.primaryBorderColor,this.specialStateColor="#f4f4f4",this.errorBkgColor=this.errorBkgColor||this.tertiaryColor,this.errorTextColor=this.errorTextColor||this.tertiaryTextColor,this.fillType0=this.primaryColor,this.fillType1=this.secondaryColor,this.fillType2=xn(this.primaryColor,{h:64}),this.fillType3=xn(this.secondaryColor,{h:64}),this.fillType4=xn(this.primaryColor,{h:-64}),this.fillType5=xn(this.secondaryColor,{h:-64}),this.fillType6=xn(this.primaryColor,{h:128}),this.fillType7=xn(this.secondaryColor,{h:128}),this.cScale1=this.cScale1||"#0b0000",this.cScale2=this.cScale2||"#4d1037",this.cScale3=this.cScale3||"#3f5258",this.cScale4=this.cScale4||"#4f2f1b",this.cScale5=this.cScale5||"#6e0a0a",this.cScale6=this.cScale6||"#3b0048",this.cScale7=this.cScale7||"#995a01",this.cScale8=this.cScale8||"#154706",this.cScale9=this.cScale9||"#161722",this.cScale10=this.cScale10||"#00296f",this.cScale11=this.cScale11||"#01629c",this.cScale12=this.cScale12||"#010029",this.cScale0=this.cScale0||this.primaryColor,this.cScale1=this.cScale1||this.secondaryColor,this.cScale2=this.cScale2||this.tertiaryColor,this.cScale3=this.cScale3||xn(this.primaryColor,{h:30}),this.cScale4=this.cScale4||xn(this.primaryColor,{h:60}),this.cScale5=this.cScale5||xn(this.primaryColor,{h:90}),this.cScale6=this.cScale6||xn(this.primaryColor,{h:120}),this.cScale7=this.cScale7||xn(this.primaryColor,{h:150}),this.cScale8=this.cScale8||xn(this.primaryColor,{h:210}),this.cScale9=this.cScale9||xn(this.primaryColor,{h:270}),this.cScale10=this.cScale10||xn(this.primaryColor,{h:300}),this.cScale11=this.cScale11||xn(this.primaryColor,{h:330});for(let N=0;N{this[p]=a[p]}),this.updateColors(),f.forEach(p=>{this[p]=a[p]})}};const pCe=i=>{const a=new gCe;return a.calculate(i),a};let bCe=class{constructor(){this.background="#f4f4f4",this.primaryColor="#ECECFF",this.secondaryColor=xn(this.primaryColor,{h:120}),this.secondaryColor="#ffffde",this.tertiaryColor=xn(this.primaryColor,{h:-160}),this.primaryBorderColor=lg(this.primaryColor,this.darkMode),this.secondaryBorderColor=lg(this.secondaryColor,this.darkMode),this.tertiaryBorderColor=lg(this.tertiaryColor,this.darkMode),this.primaryTextColor=Di(this.primaryColor),this.secondaryTextColor=Di(this.secondaryColor),this.tertiaryTextColor=Di(this.tertiaryColor),this.lineColor=Di(this.background),this.textColor=Di(this.background),this.background="white",this.mainBkg="#ECECFF",this.secondBkg="#ffffde",this.lineColor="#333333",this.border1="#9370DB",this.border2="#aaaa33",this.arrowheadColor="#333333",this.fontFamily='"trebuchet ms", verdana, arial, sans-serif',this.fontSize="16px",this.labelBackground="#e8e8e8",this.textColor="#333",this.THEME_COLOR_LIMIT=12,this.nodeBkg="calculated",this.nodeBorder="calculated",this.clusterBkg="calculated",this.clusterBorder="calculated",this.defaultLinkColor="calculated",this.titleColor="calculated",this.edgeLabelBackground="calculated",this.actorBorder="calculated",this.actorBkg="calculated",this.actorTextColor="black",this.actorLineColor="grey",this.signalColor="calculated",this.signalTextColor="calculated",this.labelBoxBkgColor="calculated",this.labelBoxBorderColor="calculated",this.labelTextColor="calculated",this.loopTextColor="calculated",this.noteBorderColor="calculated",this.noteBkgColor="#fff5ad",this.noteTextColor="calculated",this.activationBorderColor="#666",this.activationBkgColor="#f4f4f4",this.sequenceNumberColor="white",this.sectionBkgColor="calculated",this.altSectionBkgColor="calculated",this.sectionBkgColor2="calculated",this.excludeBkgColor="#eeeeee",this.taskBorderColor="calculated",this.taskBkgColor="calculated",this.taskTextLightColor="calculated",this.taskTextColor=this.taskTextLightColor,this.taskTextDarkColor="calculated",this.taskTextOutsideColor=this.taskTextDarkColor,this.taskTextClickableColor="calculated",this.activeTaskBorderColor="calculated",this.activeTaskBkgColor="calculated",this.gridColor="calculated",this.doneTaskBkgColor="calculated",this.doneTaskBorderColor="calculated",this.critBorderColor="calculated",this.critBkgColor="calculated",this.todayLineColor="calculated",this.sectionBkgColor=FA(102,102,255,.49),this.altSectionBkgColor="white",this.sectionBkgColor2="#fff400",this.taskBorderColor="#534fbc",this.taskBkgColor="#8a90dd",this.taskTextLightColor="white",this.taskTextColor="calculated",this.taskTextDarkColor="black",this.taskTextOutsideColor="calculated",this.taskTextClickableColor="#003163",this.activeTaskBorderColor="#534fbc",this.activeTaskBkgColor="#bfc7ff",this.gridColor="lightgrey",this.doneTaskBkgColor="lightgrey",this.doneTaskBorderColor="grey",this.critBorderColor="#ff8888",this.critBkgColor="red",this.todayLineColor="red",this.personBorder=this.primaryBorderColor,this.personBkg=this.mainBkg,this.labelColor="black",this.errorBkgColor="#552222",this.errorTextColor="#552222",this.updateColors()}updateColors(){var a,f,p,w,m,b,E,_,A,I,B;this.cScale0=this.cScale0||this.primaryColor,this.cScale1=this.cScale1||this.secondaryColor,this.cScale2=this.cScale2||this.tertiaryColor,this.cScale3=this.cScale3||xn(this.primaryColor,{h:30}),this.cScale4=this.cScale4||xn(this.primaryColor,{h:60}),this.cScale5=this.cScale5||xn(this.primaryColor,{h:90}),this.cScale6=this.cScale6||xn(this.primaryColor,{h:120}),this.cScale7=this.cScale7||xn(this.primaryColor,{h:150}),this.cScale8=this.cScale8||xn(this.primaryColor,{h:210}),this.cScale9=this.cScale9||xn(this.primaryColor,{h:270}),this.cScale10=this.cScale10||xn(this.primaryColor,{h:300}),this.cScale11=this.cScale11||xn(this.primaryColor,{h:330}),this["cScalePeer1"]=this["cScalePeer1"]||$s(this.secondaryColor,45),this["cScalePeer2"]=this["cScalePeer2"]||$s(this.tertiaryColor,40);for(let N=0;N{this[p]=a[p]}),this.updateColors(),f.forEach(p=>{this[p]=a[p]})}};const X1t=i=>{const a=new bCe;return a.calculate(i),a};let wCe=class{constructor(){this.background="#f4f4f4",this.primaryColor="#cde498",this.secondaryColor="#cdffb2",this.background="white",this.mainBkg="#cde498",this.secondBkg="#cdffb2",this.lineColor="green",this.border1="#13540c",this.border2="#6eaa49",this.arrowheadColor="green",this.fontFamily='"trebuchet ms", verdana, arial, sans-serif',this.fontSize="16px",this.tertiaryColor=bs("#cde498",10),this.primaryBorderColor=lg(this.primaryColor,this.darkMode),this.secondaryBorderColor=lg(this.secondaryColor,this.darkMode),this.tertiaryBorderColor=lg(this.tertiaryColor,this.darkMode),this.primaryTextColor=Di(this.primaryColor),this.secondaryTextColor=Di(this.secondaryColor),this.tertiaryTextColor=Di(this.primaryColor),this.lineColor=Di(this.background),this.textColor=Di(this.background),this.THEME_COLOR_LIMIT=12,this.nodeBkg="calculated",this.nodeBorder="calculated",this.clusterBkg="calculated",this.clusterBorder="calculated",this.defaultLinkColor="calculated",this.titleColor="#333",this.edgeLabelBackground="#e8e8e8",this.actorBorder="calculated",this.actorBkg="calculated",this.actorTextColor="black",this.actorLineColor="grey",this.signalColor="#333",this.signalTextColor="#333",this.labelBoxBkgColor="calculated",this.labelBoxBorderColor="#326932",this.labelTextColor="calculated",this.loopTextColor="calculated",this.noteBorderColor="calculated",this.noteBkgColor="#fff5ad",this.noteTextColor="calculated",this.activationBorderColor="#666",this.activationBkgColor="#f4f4f4",this.sequenceNumberColor="white",this.sectionBkgColor="#6eaa49",this.altSectionBkgColor="white",this.sectionBkgColor2="#6eaa49",this.excludeBkgColor="#eeeeee",this.taskBorderColor="calculated",this.taskBkgColor="#487e3a",this.taskTextLightColor="white",this.taskTextColor="calculated",this.taskTextDarkColor="black",this.taskTextOutsideColor="calculated",this.taskTextClickableColor="#003163",this.activeTaskBorderColor="calculated",this.activeTaskBkgColor="calculated",this.gridColor="lightgrey",this.doneTaskBkgColor="lightgrey",this.doneTaskBorderColor="grey",this.critBorderColor="#ff8888",this.critBkgColor="red",this.todayLineColor="red",this.personBorder=this.primaryBorderColor,this.personBkg=this.mainBkg,this.labelColor="black",this.errorBkgColor="#552222",this.errorTextColor="#552222"}updateColors(){var a,f,p,w,m,b,E,_,A,I,B;this.actorBorder=$s(this.mainBkg,20),this.actorBkg=this.mainBkg,this.labelBoxBkgColor=this.actorBkg,this.labelTextColor=this.actorTextColor,this.loopTextColor=this.actorTextColor,this.noteBorderColor=this.border2,this.noteTextColor=this.actorTextColor,this.cScale0=this.cScale0||this.primaryColor,this.cScale1=this.cScale1||this.secondaryColor,this.cScale2=this.cScale2||this.tertiaryColor,this.cScale3=this.cScale3||xn(this.primaryColor,{h:30}),this.cScale4=this.cScale4||xn(this.primaryColor,{h:60}),this.cScale5=this.cScale5||xn(this.primaryColor,{h:90}),this.cScale6=this.cScale6||xn(this.primaryColor,{h:120}),this.cScale7=this.cScale7||xn(this.primaryColor,{h:150}),this.cScale8=this.cScale8||xn(this.primaryColor,{h:210}),this.cScale9=this.cScale9||xn(this.primaryColor,{h:270}),this.cScale10=this.cScale10||xn(this.primaryColor,{h:300}),this.cScale11=this.cScale11||xn(this.primaryColor,{h:330}),this["cScalePeer1"]=this["cScalePeer1"]||$s(this.secondaryColor,45),this["cScalePeer2"]=this["cScalePeer2"]||$s(this.tertiaryColor,40);for(let N=0;N{this[p]=a[p]}),this.updateColors(),f.forEach(p=>{this[p]=a[p]})}};const vCe=i=>{const a=new wCe;return a.calculate(i),a};class mCe{constructor(){this.primaryColor="#eee",this.contrast="#707070",this.secondaryColor=bs(this.contrast,55),this.background="#ffffff",this.tertiaryColor=xn(this.primaryColor,{h:-160}),this.primaryBorderColor=lg(this.primaryColor,this.darkMode),this.secondaryBorderColor=lg(this.secondaryColor,this.darkMode),this.tertiaryBorderColor=lg(this.tertiaryColor,this.darkMode),this.primaryTextColor=Di(this.primaryColor),this.secondaryTextColor=Di(this.secondaryColor),this.tertiaryTextColor=Di(this.tertiaryColor),this.lineColor=Di(this.background),this.textColor=Di(this.background),this.mainBkg="#eee",this.secondBkg="calculated",this.lineColor="#666",this.border1="#999",this.border2="calculated",this.note="#ffa",this.text="#333",this.critical="#d42",this.done="#bbb",this.arrowheadColor="#333333",this.fontFamily='"trebuchet ms", verdana, arial, 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76:this.$="";break}},table:[{3:1,4:2,5:3,6:[1,5],7:[1,6],8:[1,7],9:[1,8],10:4,11:[1,9],15:[1,10],16:[1,11],17:[1,12],18:[1,13]},{1:[3]},{1:[2,1]},{1:[2,2]},{1:[2,7]},{1:[2,3]},{1:[2,4]},{1:[2,5]},{1:[2,6]},{12:[1,14]},{12:[1,15]},{12:[1,16]},{12:[1,17]},{12:[1,18]},{13:19,19:20,20:21,21:22,22:a,23:f,24:p,26:w,28:m,29:49,30:61,32:62,34:b,36:E,37:_,38:A,39:I,40:B,41:N,43:23,44:R,45:z,46:W,47:et,48:st,49:at,50:bt,51:mt,52:yt,53:ft,54:ut,55:vt,56:X,57:pt,58:U,59:Tt,60:nt,61:It,62:Ot,63:Bt,64:Et,65:Z,66:Ct,67:xt,68:Ht,69:Le,70:Ft,71:gn,72:Se,73:me,74:Ve},{13:70,19:20,20:21,21:22,22:a,23:f,24:p,26:w,28:m,29:49,30:61,32:62,34:b,36:E,37:_,38:A,39:I,40:B,41:N,43:23,44:R,45:z,46:W,47:et,48:st,49:at,50:bt,51:mt,52:yt,53:ft,54:ut,55:vt,56:X,57:pt,58:U,59:Tt,60:nt,61:It,62:Ot,63:Bt,64:Et,65:Z,66:Ct,67:xt,68:Ht,69:Le,70:Ft,71:gn,72:Se,73:me,74:Ve},{13:71,19:20,20:21,21:22,22:a,23:f,24:p,26:w,28:m,29:49,30:61,32:62,34:b,36:E,37:_,38:A,39:I,40:B,41:N,43:23,44:R,45:z,46:W,47:et,48:st,49:at,50:bt,51:mt,52:yt,53:ft,54:ut,55:vt,56:X,57:pt,58:U,59:Tt,60:nt,61:It,62:Ot,63:Bt,64:Et,65:Z,66:Ct,67:xt,68:Ht,69:Le,70:Ft,71:gn,72:Se,73:me,74:Ve},{13:72,19:20,20:21,21:22,22:a,23:f,24:p,26:w,28:m,29:49,30:61,32:62,34:b,36:E,37:_,38:A,39:I,40:B,41:N,43:23,44:R,45:z,46:W,47:et,48:st,49:at,50:bt,51:mt,52:yt,53:ft,54:ut,55:vt,56:X,57:pt,58:U,59:Tt,60:nt,61:It,62:Ot,63:Bt,64:Et,65:Z,66:Ct,67:xt,68:Ht,69:Le,70:Ft,71:gn,72:Se,73:me,74:Ve},{13:73,19:20,20:21,21:22,22:a,23:f,24:p,26:w,28:m,29:49,30:61,32:62,34:b,36:E,37:_,38:A,39:I,40:B,41:N,43:23,44:R,45:z,46:W,47:et,48:st,49:at,50:bt,51:mt,52:yt,53:ft,54:ut,55:vt,56:X,57:pt,58:U,59:Tt,60:nt,61:It,62:Ot,63:Bt,64:Et,65:Z,66:Ct,67:xt,68:Ht,69:Le,70:Ft,71:gn,72:Se,73:me,74:Ve},{14:[1,74]},i(Ye,[2,13],{43:23,29:49,30:61,32:62,20:75,34:b,36:E,37:_,38:A,39:I,40:B,41:N,44:R,45:z,46:W,47:et,48:st,49:at,50:bt,51:mt,52:yt,53:ft,54:ut,55:vt,56:X,57:pt,58:U,59:Tt,60:nt,61:It,62:Ot,63:Bt,64:Et,65:Z,66:Ct,67:xt,68:Ht,69:Le,70:Ft,71:gn,72:Se,73:me,74:Ve}),i(Ye,[2,14]),i(ce,[2,16],{12:[1,76]}),i(Ye,[2,36],{12:[1,77]}),i(ke,[2,19]),i(ke,[2,20]),{25:[1,78]},{27:[1,79]},i(ke,[2,23]),{35:80,75:81,76:zt,77:re,79:se,80:Pe},{35:86,75:81,76:zt,77:re,79:se,80:Pe},{35:87,75:81,76:zt,77:re,79:se,80:Pe},{35:88,75:81,76:zt,77:re,79:se,80:Pe},{35:89,75:81,76:zt,77:re,79:se,80:Pe},{35:90,75:81,76:zt,77:re,79:se,80:Pe},{35:91,75:81,76:zt,77:re,79:se,80:Pe},{35:92,75:81,76:zt,77:re,79:se,80:Pe},{35:93,75:81,76:zt,77:re,79:se,80:Pe},{35:94,75:81,76:zt,77:re,79:se,80:Pe},{35:95,75:81,76:zt,77:re,79:se,80:Pe},{35:96,75:81,76:zt,77:re,79:se,80:Pe},{35:97,75:81,76:zt,77:re,79:se,80:Pe},{35:98,75:81,76:zt,77:re,79:se,80:Pe},{35:99,75:81,76:zt,77:re,79:se,80:Pe},{35:100,75:81,76:zt,77:re,79:se,80:Pe},{35:101,75:81,76:zt,77:re,79:se,80:Pe},{35:102,75:81,76:zt,77:re,79:se,80:Pe},{35:103,75:81,76:zt,77:re,79:se,80:Pe},{35:104,75:81,76:zt,77:re,79:se,80:Pe},i(te,[2,59]),{35:105,75:81,76:zt,77:re,79:se,80:Pe},{35:106,75:81,76:zt,77:re,79:se,80:Pe},{35:107,75:81,76:zt,77:re,79:se,80:Pe},{35:108,75:81,76:zt,77:re,79:se,80:Pe},{35:109,75:81,76:zt,77:re,79:se,80:Pe},{35:110,75:81,76:zt,77:re,79:se,80:Pe},{35:111,75:81,76:zt,77:re,79:se,80:Pe},{35:112,75:81,76:zt,77:re,79:se,80:Pe},{35:113,75:81,76:zt,77:re,79:se,80:Pe},{35:114,75:81,76:zt,77:re,79:se,80:Pe},{35:115,75:81,76:zt,77:re,79:se,80:Pe},{20:116,29:49,30:61,32:62,34:b,36:E,37:_,38:A,39:I,40:B,41:N,43:23,44:R,45:z,46:W,47:et,48:st,49:at,50:bt,51:mt,52:yt,53:ft,54:ut,55:vt,56:X,57:pt,58:U,59:Tt,60:nt,61:It,62:Ot,63:Bt,64:Et,65:Z,66:Ct,67:xt,68:Ht,69:Le,70:Ft,71:gn,72:Se,73:me,74:Ve},{12:[1,118],33:[1,117]},{35:119,75:81,76:zt,77:re,79:se,80:Pe},{35:120,75:81,76:zt,77:re,79:se,80:Pe},{35:121,75:81,76:zt,77:re,79:se,80:Pe},{35:122,75:81,76:zt,77:re,79:se,80:Pe},{35:123,75:81,76:zt,77:re,79:se,80:Pe},{35:124,75:81,76:zt,77:re,79:se,80:Pe},{35:125,75:81,76:zt,77:re,79:se,80:Pe},{14:[1,126]},{14:[1,127]},{14:[1,128]},{14:[1,129]},{1:[2,8]},i(Ye,[2,15]),i(ce,[2,17],{21:22,19:130,22:a,23:f,24:p,26:w,28:m}),i(Ye,[2,37],{19:20,20:21,21:22,43:23,29:49,30:61,32:62,13:131,22:a,23:f,24:p,26:w,28:m,34:b,36:E,37:_,38:A,39:I,40:B,41:N,44:R,45:z,46:W,47:et,48:st,49:at,50:bt,51:mt,52:yt,53:ft,54:ut,55:vt,56:X,57:pt,58:U,59:Tt,60:nt,61:It,62:Ot,63:Bt,64:Et,65:Z,66:Ct,67:xt,68:Ht,69:Le,70:Ft,71:gn,72:Se,73:me,74:Ve}),i(ke,[2,21]),i(ke,[2,22]),i(te,[2,39]),i(Me,[2,71],{75:81,35:132,76:zt,77:re,79:se,80:Pe}),i(de,[2,73]),{78:[1,133]},i(de,[2,75]),i(de,[2,76]),i(te,[2,40]),i(te,[2,41]),i(te,[2,42]),i(te,[2,43]),i(te,[2,44]),i(te,[2,45]),i(te,[2,46]),i(te,[2,47]),i(te,[2,48]),i(te,[2,49]),i(te,[2,50]),i(te,[2,51]),i(te,[2,52]),i(te,[2,53]),i(te,[2,54]),i(te,[2,55]),i(te,[2,56]),i(te,[2,57]),i(te,[2,58]),i(te,[2,60]),i(te,[2,61]),i(te,[2,62]),i(te,[2,63]),i(te,[2,64]),i(te,[2,65]),i(te,[2,66]),i(te,[2,67]),i(te,[2,68]),i(te,[2,69]),i(te,[2,70]),{31:134,42:[1,135]},{12:[1,136]},{33:[1,137]},i(on,[2,28]),i(on,[2,29]),i(on,[2,30]),i(on,[2,31]),i(on,[2,32]),i(on,[2,33]),i(on,[2,34]),{1:[2,9]},{1:[2,10]},{1:[2,11]},{1:[2,12]},i(ce,[2,18]),i(Ye,[2,38]),i(Me,[2,72]),i(de,[2,74]),i(te,[2,24]),i(te,[2,35]),i(ni,[2,25]),i(ni,[2,26],{12:[1,138]}),i(ni,[2,27])],defaultActions:{2:[2,1],3:[2,2],4:[2,7],5:[2,3],6:[2,4],7:[2,5],8:[2,6],74:[2,8],126:[2,9],127:[2,10],128:[2,11],129:[2,12]},parseError:function(Er,Xn){if(Xn.recoverable)this.trace(Er);else{var di=new Error(Er);throw di.hash=Xn,di}},parse:function(Er){var Xn=this,di=[0],Ee=[],Kn=[null],He=[],Ti=this.table,pn="",Es=0,qa=0,Ma=2,Gs=1,Po=He.slice.call(arguments,1),vs=Object.create(this.lexer),ru={yy:{}};for(var zs in this.yy)Object.prototype.hasOwnProperty.call(this.yy,zs)&&(ru.yy[zs]=this.yy[zs]);vs.setInput(Er,ru.yy),ru.yy.lexer=vs,ru.yy.parser=this,typeof vs.yylloc>"u"&&(vs.yylloc={});var Du=vs.yylloc;He.push(Du);var pm=vs.options&&vs.options.ranges;typeof ru.yy.parseError=="function"?this.parseError=ru.yy.parseError:this.parseError=Object.getPrototypeOf(this).parseError;function uw(){var Dl;return Dl=Ee.pop()||vs.lex()||Gs,typeof Dl!="number"&&(Dl instanceof Array&&(Ee=Dl,Dl=Ee.pop()),Dl=Xn.symbols_[Dl]||Dl),Dl}for(var Wu,th,Fa,Ml,ha={},bc,Cc,pa,Da;;){if(th=di[di.length-1],this.defaultActions[th]?Fa=this.defaultActions[th]:((Wu===null||typeof Wu>"u")&&(Wu=uw()),Fa=Ti[th]&&Ti[th][Wu]),typeof Fa>"u"||!Fa.length||!Fa[0]){var Ha="";Da=[];for(bc in 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this.yy=Xn||this.yy||{},this._input=Er,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var Er=this._input[0];this.yytext+=Er,this.yyleng++,this.offset++,this.match+=Er,this.matched+=Er;var Xn=Er.match(/(?:\r\n?|\n).*/g);return Xn?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),Er},unput:function(Er){var Xn=Er.length,di=Er.split(/(?:\r\n?|\n)/g);this._input=Er+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-Xn),this.offset-=Xn;var Ee=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),di.length-1&&(this.yylineno-=di.length-1);var Kn=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:di?(di.length===Ee.length?this.yylloc.first_column:0)+Ee[Ee.length-di.length].length-di[0].length:this.yylloc.first_column-Xn},this.options.ranges&&(this.yylloc.range=[Kn[0],Kn[0]+this.yyleng-Xn]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){if(this.options.backtrack_lexer)this._backtrack=!0;else return this.parseError("Lexical error on line "+(this.yylineno+1)+`. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true). +`+this.showPosition(),{text:"",token:null,line:this.yylineno});return this},less:function(Er){this.unput(this.match.slice(Er))},pastInput:function(){var Er=this.matched.substr(0,this.matched.length-this.match.length);return(Er.length>20?"...":"")+Er.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var Er=this.match;return Er.length<20&&(Er+=this._input.substr(0,20-Er.length)),(Er.substr(0,20)+(Er.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var Er=this.pastInput(),Xn=new Array(Er.length+1).join("-");return Er+this.upcomingInput()+` +`+Xn+"^"},test_match:function(Er,Xn){var di,Ee,Kn;if(this.options.backtrack_lexer&&(Kn={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(Kn.yylloc.range=this.yylloc.range.slice(0))),Ee=Er[0].match(/(?:\r\n?|\n).*/g),Ee&&(this.yylineno+=Ee.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:Ee?Ee[Ee.length-1].length-Ee[Ee.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+Er[0].length},this.yytext+=Er[0],this.match+=Er[0],this.matches=Er,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(Er[0].length),this.matched+=Er[0],di=this.performAction.call(this,this.yy,this,Xn,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),di)return di;if(this._backtrack){for(var He in Kn)this[He]=Kn[He];return!1}return!1},next:function(){if(this.done)return this.EOF;this._input||(this.done=!0);var Er,Xn,di,Ee;this._more||(this.yytext="",this.match="");for(var Kn=this._currentRules(),He=0;HeXn[0].length)){if(Xn=di,Ee=He,this.options.backtrack_lexer){if(Er=this.test_match(di,Kn[He]),Er!==!1)return Er;if(this._backtrack){Xn=!1;continue}else return!1}else if(!this.options.flex)break}return Xn?(Er=this.test_match(Xn,Kn[Ee]),Er!==!1?Er:!1):this._input===""?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+`. Unrecognized text. +`+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){var Xn=this.next();return Xn||this.lex()},begin:function(Xn){this.conditionStack.push(Xn)},popState:function(){var Xn=this.conditionStack.length-1;return Xn>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(Xn){return Xn=this.conditionStack.length-1-Math.abs(Xn||0),Xn>=0?this.conditionStack[Xn]:"INITIAL"},pushState:function(Xn){this.begin(Xn)},stateStackSize:function(){return this.conditionStack.length},options:{},performAction:function(Xn,di,Ee,Kn){switch(Ee){case 0:return 6;case 1:return 7;case 2:return 8;case 3:return 9;case 4:return 22;case 5:return 23;case 6:return this.begin("acc_title"),24;case 7:return this.popState(),"acc_title_value";case 8:return this.begin("acc_descr"),26;case 9:return this.popState(),"acc_descr_value";case 10:this.begin("acc_descr_multiline");break;case 11:this.popState();break;case 12:return"acc_descr_multiline_value";case 13:break;case 14:c;break;case 15:return 12;case 16:break;case 17:return 11;case 18:return 15;case 19:return 16;case 20:return 17;case 21:return 18;case 22:return this.begin("person_ext"),45;case 23:return this.begin("person"),44;case 24:return this.begin("system_ext_queue"),51;case 25:return this.begin("system_ext_db"),50;case 26:return this.begin("system_ext"),49;case 27:return this.begin("system_queue"),48;case 28:return this.begin("system_db"),47;case 29:return this.begin("system"),46;case 30:return this.begin("boundary"),37;case 31:return this.begin("enterprise_boundary"),34;case 32:return this.begin("system_boundary"),36;case 33:return this.begin("container_ext_queue"),57;case 34:return this.begin("container_ext_db"),56;case 35:return this.begin("container_ext"),55;case 36:return 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zdt=function(i){Z1(ds,i),i.fontFamily&&(ds.personFontFamily=ds.systemFontFamily=ds.messageFontFamily=i.fontFamily),i.fontSize&&(ds.personFontSize=ds.systemFontSize=ds.messageFontSize=i.fontSize),i.fontWeight&&(ds.personFontWeight=ds.systemFontWeight=ds.messageFontWeight=i.fontWeight)},hF=(i,a)=>({fontFamily:i[a+"FontFamily"],fontSize:i[a+"FontSize"],fontWeight:i[a+"FontWeight"]}),nY=i=>({fontFamily:i.boundaryFontFamily,fontSize:i.boundaryFontSize,fontWeight:i.boundaryFontWeight}),JDe=i=>({fontFamily:i.messageFontFamily,fontSize:i.messageFontSize,fontWeight:i.messageFontWeight});function cm(i,a,f,p,w){if(!a[i].width)if(f)a[i].text=UIt(a[i].text,w,p),a[i].textLines=a[i].text.split(Kr.lineBreakRegex).length,a[i].width=w,a[i].height=odt(a[i].text,p);else{let m=a[i].text.split(Kr.lineBreakRegex);a[i].textLines=m.length;let b=0;a[i].height=0,a[i].width=0;for(const E of m)a[i].width=Math.max(d3(E,p),a[i].width),b=odt(E,p),a[i].height=a[i].height+b}}const EPt=function(i,a,f){a.x=f.data.startx,a.y=f.data.starty,a.width=f.data.stopx-f.data.startx,a.height=f.data.stopy-f.data.starty,a.label.y=ds.c4ShapeMargin-35;let p=a.wrap&&ds.wrap,w=nY(ds);w.fontSize=w.fontSize+2,w.fontWeight="bold";let m=d3(a.label.text,w);cm("label",a,p,w,m),b3.drawBoundary(i,a,ds)},TPt=function(i,a,f,p){let w=0;for(const m of p){w=0;const b=f[m];let E=hF(ds,b.typeC4Shape.text);switch(E.fontSize=E.fontSize-2,b.typeC4Shape.width=d3("«"+b.typeC4Shape.text+"»",E),b.typeC4Shape.height=E.fontSize+2,b.typeC4Shape.Y=ds.c4ShapePadding,w=b.typeC4Shape.Y+b.typeC4Shape.height-4,b.image={width:0,height:0,Y:0},b.typeC4Shape.text){case"person":case"external_person":b.image.width=48,b.image.height=48,b.image.Y=w,w=b.image.Y+b.image.height;break}b.sprite&&(b.image.width=48,b.image.height=48,b.image.Y=w,w=b.image.Y+b.image.height);let _=b.wrap&&ds.wrap,A=ds.width-ds.c4ShapePadding*2,I=hF(ds,b.typeC4Shape.text);if(I.fontSize=I.fontSize+2,I.fontWeight="bold",cm("label",b,_,I,A),b.label.Y=w+8,w=b.label.Y+b.label.height,b.type&&b.type.text!==""){b.type.text="["+b.type.text+"]";let R=hF(ds,b.typeC4Shape.text);cm("type",b,_,R,A),b.type.Y=w+5,w=b.type.Y+b.type.height}else if(b.techn&&b.techn.text!==""){b.techn.text="["+b.techn.text+"]";let R=hF(ds,b.techn.text);cm("techn",b,_,R,A),b.techn.Y=w+5,w=b.techn.Y+b.techn.height}let B=w,N=b.label.width;if(b.descr&&b.descr.text!==""){let R=hF(ds,b.typeC4Shape.text);cm("descr",b,_,R,A),b.descr.Y=w+20,w=b.descr.Y+b.descr.height,N=Math.max(b.label.width,b.descr.width),B=w-b.descr.textLines*5}N=N+ds.c4ShapePadding,b.width=Math.max(b.width||ds.width,N,ds.width),b.height=Math.max(b.height||ds.height,B,ds.height),b.margin=b.margin||ds.c4ShapeMargin,i.insert(b),b3.drawC4Shape(a,b,ds)}i.bumpLastMargin(ds.c4ShapeMargin)};let rw=class{constructor(a,f){this.x=a,this.y=f}},CPt=function(i,a){let f=i.x,p=i.y,w=a.x,m=a.y,b=f+i.width/2,E=p+i.height/2,_=Math.abs(f-w),A=Math.abs(p-m),I=A/_,B=i.height/i.width,N=null;return p==m&&fw?N=new rw(f,E):f==w&&pm&&(N=new rw(b,p)),f>w&&p=I?N=new rw(f,E+I*i.width/2):N=new rw(b-_/A*i.height/2,p+i.height):f=I?N=new rw(f+i.width,E+I*i.width/2):N=new rw(b+_/A*i.height/2,p+i.height):fm?B>=I?N=new rw(f+i.width,E-I*i.width/2):N=new rw(b+i.height/2*_/A,p):f>w&&p>m&&(B>=I?N=new rw(f,E-i.width/2*I):N=new rw(b-i.height/2*_/A,p)),N},tIe=function(i,a){let f={x:0,y:0};f.x=a.x+a.width/2,f.y=a.y+a.height/2;let p=CPt(i,f);f.x=i.x+i.width/2,f.y=i.y+i.height/2;let w=CPt(a,f);return{startPoint:p,endPoint:w}};const eIe=function(i,a,f,p){let w=0;for(let m of a){w=w+1;let b=m.wrap&&ds.wrap,E=JDe(ds);p.db.getC4Type()==="C4Dynamic"&&(m.label.text=w+": "+m.label.text);let A=d3(m.label.text,E);cm("label",m,b,E,A),m.techn&&m.techn.text!==""&&(A=d3(m.techn.text,E),cm("techn",m,b,E,A)),m.descr&&m.descr.text!==""&&(A=d3(m.descr.text,E),cm("descr",m,b,E,A));let I=f(m.from),B=f(m.to),N=tIe(I,B);m.startPoint=N.startPoint,m.endPoint=N.endPoint}b3.drawRels(i,a,ds)};function _Pt(i,a,f,p,w){let m=new kPt(w);m.data.widthLimit=f.data.widthLimit/Math.min($dt,p.length);for(let[b,E]of p.entries()){let _=0;E.image={width:0,height:0,Y:0},E.sprite&&(E.image.width=48,E.image.height=48,E.image.Y=_,_=E.image.Y+E.image.height);let A=E.wrap&&ds.wrap,I=nY(ds);if(I.fontSize=I.fontSize+2,I.fontWeight="bold",cm("label",E,A,I,m.data.widthLimit),E.label.Y=_+8,_=E.label.Y+E.label.height,E.type&&E.type.text!==""){E.type.text="["+E.type.text+"]";let z=nY(ds);cm("type",E,A,z,m.data.widthLimit),E.type.Y=_+5,_=E.type.Y+E.type.height}if(E.descr&&E.descr.text!==""){let z=nY(ds);z.fontSize=z.fontSize-2,cm("descr",E,A,z,m.data.widthLimit),E.descr.Y=_+20,_=E.descr.Y+E.descr.height}if(b==0||b%$dt===0){let z=f.data.startx+ds.diagramMarginX,W=f.data.stopy+ds.diagramMarginY+_;m.setData(z,z,W,W)}else{let z=m.data.stopx!==m.data.startx?m.data.stopx+ds.diagramMarginX:m.data.startx,W=m.data.starty;m.setData(z,z,W,W)}m.name=E.alias;let B=w.db.getC4ShapeArray(E.alias),N=w.db.getC4ShapeKeys(E.alias);N.length>0&&TPt(m,i,B,N),a=E.alias;let R=w.db.getBoundarys(a);R.length>0&&_Pt(i,a,m,R,w),E.alias!=="global"&&EPt(i,E,m),f.data.stopy=Math.max(m.data.stopy+ds.c4ShapeMargin,f.data.stopy),f.data.stopx=Math.max(m.data.stopx+ds.c4ShapeMargin,f.data.stopx),tY=Math.max(tY,f.data.stopx),eY=Math.max(eY,f.data.stopy)}}const SPt={drawPersonOrSystemArray:TPt,drawBoundary:EPt,setConf:zdt,draw:function(i,a,f,p){ds=Oe().c4;const w=Oe().securityLevel;let m;w==="sandbox"&&(m=yr("#i"+a));const b=yr(w==="sandbox"?m.nodes()[0].contentDocument.body:"body");let E=p.db;p.db.setWrap(ds.wrap),xPt=E.getC4ShapeInRow(),$dt=E.getC4BoundaryInRow(),Ut.debug(`C:${JSON.stringify(ds,null,2)}`);const 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this.yy=Ts||this.yy||{},this._input=Qi,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var Qi=this._input[0];this.yytext+=Qi,this.yyleng++,this.offset++,this.match+=Qi,this.matched+=Qi;var Ts=Qi.match(/(?:\r\n?|\n).*/g);return Ts?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),Qi},unput:function(Qi){var Ts=Qi.length,ka=Qi.split(/(?:\r\n?|\n)/g);this._input=Qi+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-Ts),this.offset-=Ts;var xi=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),ka.length-1&&(this.yylineno-=ka.length-1);var Yc=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:ka?(ka.length===xi.length?this.yylloc.first_column:0)+xi[xi.length-ka.length].length-ka[0].length:this.yylloc.first_column-Ts},this.options.ranges&&(this.yylloc.range=[Yc[0],Yc[0]+this.yyleng-Ts]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){if(this.options.backtrack_lexer)this._backtrack=!0;else return this.parseError("Lexical error on line "+(this.yylineno+1)+`. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true). +`+this.showPosition(),{text:"",token:null,line:this.yylineno});return this},less:function(Qi){this.unput(this.match.slice(Qi))},pastInput:function(){var Qi=this.matched.substr(0,this.matched.length-this.match.length);return(Qi.length>20?"...":"")+Qi.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var Qi=this.match;return Qi.length<20&&(Qi+=this._input.substr(0,20-Qi.length)),(Qi.substr(0,20)+(Qi.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var Qi=this.pastInput(),Ts=new Array(Qi.length+1).join("-");return Qi+this.upcomingInput()+` +`+Ts+"^"},test_match:function(Qi,Ts){var ka,xi,Yc;if(this.options.backtrack_lexer&&(Yc={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(Yc.yylloc.range=this.yylloc.range.slice(0))),xi=Qi[0].match(/(?:\r\n?|\n).*/g),xi&&(this.yylineno+=xi.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:xi?xi[xi.length-1].length-xi[xi.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+Qi[0].length},this.yytext+=Qi[0],this.match+=Qi[0],this.matches=Qi,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(Qi[0].length),this.matched+=Qi[0],ka=this.performAction.call(this,this.yy,this,Ts,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),ka)return ka;if(this._backtrack){for(var Ce in Yc)this[Ce]=Yc[Ce];return!1}return!1},next:function(){if(this.done)return this.EOF;this._input||(this.done=!0);var Qi,Ts,ka,xi;this._more||(this.yytext="",this.match="");for(var Yc=this._currentRules(),Ce=0;CeTs[0].length)){if(Ts=ka,xi=Ce,this.options.backtrack_lexer){if(Qi=this.test_match(ka,Yc[Ce]),Qi!==!1)return Qi;if(this._backtrack){Ts=!1;continue}else return!1}else if(!this.options.flex)break}return Ts?(Qi=this.test_match(Ts,Yc[xi]),Qi!==!1?Qi:!1):this._input===""?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+`. Unrecognized text. +`+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){var Ts=this.next();return Ts||this.lex()},begin:function(Ts){this.conditionStack.push(Ts)},popState:function(){var Ts=this.conditionStack.length-1;return Ts>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(Ts){return Ts=this.conditionStack.length-1-Math.abs(Ts||0),Ts>=0?this.conditionStack[Ts]:"INITIAL"},pushState:function(Ts){this.begin(Ts)},stateStackSize:function(){return this.conditionStack.length},options:{},performAction:function(Ts,ka,xi,Yc){switch(xi){case 0:return this.begin("acc_title"),34;case 1:return this.popState(),"acc_title_value";case 2:return this.begin("acc_descr"),36;case 3:return this.popState(),"acc_descr_value";case 4:this.begin("acc_descr_multiline");break;case 5:this.popState();break;case 6:return"acc_descr_multiline_value";case 7:this.begin("callbackname");break;case 8:this.popState();break;case 9:this.popState(),this.begin("callbackargs");break;case 10:return 92;case 11:this.popState();break;case 12:return 93;case 13:return"MD_STR";case 14:this.popState();break;case 15:this.begin("md_string");break;case 16:return"STR";case 17:this.popState();break;case 18:this.pushState("string");break;case 19:return 81;case 20:return 99;case 21:return 82;case 22:return 101;case 23:return 83;case 24:return 84;case 25:return 94;case 26:this.begin("click");break;case 27:this.popState();break;case 28:return 85;case 29:return Ts.lex.firstGraph()&&this.begin("dir"),12;case 30:return Ts.lex.firstGraph()&&this.begin("dir"),12;case 31:return Ts.lex.firstGraph()&&this.begin("dir"),12;case 32:return 27;case 33:return 32;case 34:return 95;case 35:return 95;case 36:return 95;case 37:return 95;case 38:return this.popState(),13;case 39:return this.popState(),14;case 40:return this.popState(),14;case 41:return this.popState(),14;case 42:return this.popState(),14;case 43:return this.popState(),14;case 44:return this.popState(),14;case 45:return this.popState(),14;case 46:return this.popState(),14;case 47:return this.popState(),14;case 48:return this.popState(),14;case 49:return 118;case 50:return 119;case 51:return 120;case 52:return 121;case 53:return 102;case 54:return 108;case 55:return 44;case 56:return 58;case 57:return 42;case 58:return 8;case 59:return 103;case 60:return 112;case 61:return this.popState(),75;case 62:return this.pushState("edgeText"),73;case 63:return 116;case 64:return this.popState(),75;case 65:return this.pushState("thickEdgeText"),73;case 66:return 116;case 67:return this.popState(),75;case 68:return this.pushState("dottedEdgeText"),73;case 69:return 116;case 70:return 75;case 71:return this.popState(),51;case 72:return"TEXT";case 73:return this.pushState("ellipseText"),50;case 74:return this.popState(),53;case 75:return this.pushState("text"),52;case 76:return this.popState(),55;case 77:return this.pushState("text"),54;case 78:return 56;case 79:return this.pushState("text"),65;case 80:return this.popState(),62;case 81:return this.pushState("text"),61;case 82:return this.popState(),47;case 83:return this.pushState("text"),46;case 84:return this.popState(),67;case 85:return this.popState(),69;case 86:return 114;case 87:return this.pushState("trapText"),66;case 88:return this.pushState("trapText"),68;case 89:return 115;case 90:return 65;case 91:return 87;case 92:return"SEP";case 93:return 86;case 94:return 112;case 95:return 108;case 96:return 42;case 97:return 106;case 98:return 111;case 99:return 113;case 100:return this.popState(),60;case 101:return this.pushState("text"),60;case 102:return this.popState(),49;case 103:return this.pushState("text"),48;case 104:return this.popState(),31;case 105:return this.pushState("text"),29;case 106:return this.popState(),64;case 107:return this.pushState("text"),63;case 108:return"TEXT";case 109:return"QUOTE";case 110:return 9;case 111:return 10;case 112:return 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E.attr("style",a.style),tf(a,E),a.intersect=function(_){return kh.polygon(a,b,_)},f},K$e=(i,a)=>{const f=i.insert("g").attr("class","node default").attr("id",a.domId||a.id),p=f.insert("circle",":first-child");return p.attr("class","state-start").attr("r",7).attr("width",14).attr("height",14),tf(a,p),a.intersect=function(w){return kh.circle(a,7,w)},f},yBt=(i,a,f)=>{const p=i.insert("g").attr("class","node default").attr("id",a.domId||a.id);let w=70,m=10;f==="LR"&&(w=10,m=70);const b=p.append("rect").attr("x",-1*w/2).attr("y",-1*m/2).attr("width",w).attr("height",m).attr("class","fork-join");return tf(a,b),a.height=a.height+a.padding/2,a.width=a.width+a.padding/2,a.intersect=function(E){return 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yr(bt).attr("transform","translate( "+(-1*I/2+ut)+", "+(-1*B/2+R)+")"),R+=mt.height+p,_.attr("class","divider").attr("x1",-I/2-f).attr("x2",I/2+f).attr("y1",-B/2-f+w+R).attr("y2",-B/2-f+w+R),R+=w,yt.forEach(vt=>{yr(vt).attr("transform","translate( "+-I/2+", "+(-1*B/2+R+w/2)+")");const X=vt==null?void 0:vt.getBBox();R+=((X==null?void 0:X.height)??0)+p}),R+=w,A.attr("class","divider").attr("x1",-I/2-f).attr("x2",I/2+f).attr("y1",-B/2-f+w+R).attr("y2",-B/2-f+w+R),R+=w,ft.forEach(vt=>{yr(vt).attr("transform","translate( "+-I/2+", "+(-1*B/2+R)+")");const X=vt==null?void 0:vt.getBBox();R+=((X==null?void 0:X.height)??0)+p}),E.attr("class","outer title-state").attr("x",-I/2-f).attr("y",-(B/2)-f).attr("width",I+a.padding).attr("height",B+a.padding),tf(a,E),a.intersect=function(vt){return kh.rect(a,vt)},b}};let cL={};const kBt=async(i,a,f)=>{let p,w;if(a.link){let 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B=_.getBBox();I.attr("transform","translate("+-B.width/2+", "+-B.height/2+")"),Bd[a.id]||(Bd[a.id]={}),Bd[a.id].startLeft=A,LY(E,a.startLabelLeft)}if(a.startLabelRight){const _=gp(a.startLabelRight,a.labelStyle),A=i.insert("g").attr("class","edgeTerminals"),I=A.insert("g").attr("class","inner");E=A.node().appendChild(_),I.node().appendChild(_);const B=_.getBBox();I.attr("transform","translate("+-B.width/2+", "+-B.height/2+")"),Bd[a.id]||(Bd[a.id]={}),Bd[a.id].startRight=A,LY(E,a.startLabelRight)}if(a.endLabelLeft){const _=gp(a.endLabelLeft,a.labelStyle),A=i.insert("g").attr("class","edgeTerminals"),I=A.insert("g").attr("class","inner");E=I.node().appendChild(_);const B=_.getBBox();I.attr("transform","translate("+-B.width/2+", "+-B.height/2+")"),A.node().appendChild(_),Bd[a.id]||(Bd[a.id]={}),Bd[a.id].endLeft=A,LY(E,a.endLabelLeft)}if(a.endLabelRight){const _=gp(a.endLabelRight,a.labelStyle),A=i.insert("g").attr("class","edgeTerminals"),I=A.insert("g").attr("class","inner");E=I.node().appendChild(_);const B=_.getBBox();I.attr("transform","translate("+-B.width/2+", "+-B.height/2+")"),A.node().appendChild(_),Bd[a.id]||(Bd[a.id]={}),Bd[a.id].endRight=A,LY(E,a.endLabelRight)}return p};function LY(i,a){Oe().flowchart.htmlLabels&&i&&(i.style.width=a.length*9+"px",i.style.height="12px")}const nze=(i,a)=>{Ut.info("Moving label abc78 ",i.id,i.label,AY[i.id]);let f=a.updatedPath?a.updatedPath:a.originalPath;if(i.label){const p=AY[i.id];let w=i.x,m=i.y;if(f){const b=$a.calcLabelPosition(f);Ut.info("Moving label "+i.label+" from (",w,",",m,") to (",b.x,",",b.y,") abc78"),a.updatedPath&&(w=b.x,m=b.y)}p.attr("transform","translate("+w+", "+m+")")}if(i.startLabelLeft){const p=Bd[i.id].startLeft;let w=i.x,m=i.y;if(f){const b=$a.calcTerminalLabelPosition(i.arrowTypeStart?10:0,"start_left",f);w=b.x,m=b.y}p.attr("transform","translate("+w+", 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40:this.$=Tt.Identification.IDENTIFYING;break}},table:[{3:1,4:[1,2]},{1:[3]},i(a,[2,2],{5:3}),{6:[1,4],7:5,8:[1,6],9:7,10:[1,8],11:9,20:f,22:p,24:w,26:m,27:b,28:E},i(a,[2,7],{1:[2,1]}),i(a,[2,3]),{9:16,11:9,20:f,22:p,24:w,26:m,27:b,28:E},i(a,[2,5]),i(a,[2,6]),i(a,[2,11],{12:17,39:20,15:[1,18],18:[1,19],41:_,42:A,43:I,44:B,45:N}),{21:[1,26]},{23:[1,27]},{25:[1,28]},i(a,[2,18]),i(R,[2,19]),i(R,[2,20]),i(a,[2,4]),{11:29,27:b,28:E},{16:30,17:[1,31],29:32,30:33,34:z},{11:35,27:b,28:E},{40:36,46:[1,37],47:[1,38]},i(W,[2,34]),i(W,[2,35]),i(W,[2,36]),i(W,[2,37]),i(W,[2,38]),i(a,[2,15]),i(a,[2,16]),i(a,[2,17]),{13:[1,39]},{17:[1,40]},i(a,[2,10]),{16:41,17:[2,21],29:32,30:33,34:z},{31:42,34:[1,43]},{34:[2,27]},{19:[1,44]},{39:45,41:_,42:A,43:I,44:B,45:N},i(et,[2,39]),i(et,[2,40]),{14:46,27:[1,49],28:[1,48],48:[1,47]},i(a,[2,9]),{17:[2,22]},i(st,[2,23],{32:50,33:51,35:52,37:at,38:bt}),i([17,34,37,38],[2,28]),i(a,[2,14],{15:[1,55]}),i([27,28],[2,33]),i(a,[2,8]),i(a,[2,41]),i(a,[2,42]),i(a,[2,43]),i(st,[2,24],{33:56,36:[1,57],38:bt}),i(st,[2,25]),i(mt,[2,29]),i(st,[2,32]),i(mt,[2,31]),{16:58,17:[1,59],29:32,30:33,34:z},i(st,[2,26]),{35:60,37:at},{17:[1,61]},i(a,[2,13]),i(mt,[2,30]),i(a,[2,12])],defaultActions:{34:[2,27],41:[2,22]},parseError:function(X,pt){if(pt.recoverable)this.trace(X);else{var 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Ot[ce])this.terminals_[se]&&se>Ct&&Me.push("'"+this.terminals_[se]+"'");Le.showPosition?de="Parse error on line "+(Et+1)+`: +`+Le.showPosition()+` +Expecting `+Me.join(", ")+", got '"+(this.terminals_[Ye]||Ye)+"'":de="Parse error on line "+(Et+1)+": Unexpected "+(Ye==xt?"end of input":"'"+(this.terminals_[Ye]||Ye)+"'"),this.parseError(de,{text:Le.match,token:this.terminals_[Ye]||Ye,line:Le.yylineno,loc:Se,expected:Me})}if(ke[0]instanceof Array&&ke.length>1)throw new Error("Parse Error: multiple actions possible at state: "+ce+", token: "+Ye);switch(ke[0]){case 1:U.push(Ye),nt.push(Le.yytext),It.push(Le.yylloc),U.push(ke[1]),Ye=null,Z=Le.yyleng,Bt=Le.yytext,Et=Le.yylineno,Se=Le.yylloc;break;case 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this.yy=pt||this.yy||{},this._input=X,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var X=this._input[0];this.yytext+=X,this.yyleng++,this.offset++,this.match+=X,this.matched+=X;var pt=X.match(/(?:\r\n?|\n).*/g);return pt?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),X},unput:function(X){var pt=X.length,U=X.split(/(?:\r\n?|\n)/g);this._input=X+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-pt),this.offset-=pt;var Tt=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),U.length-1&&(this.yylineno-=U.length-1);var nt=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:U?(U.length===Tt.length?this.yylloc.first_column:0)+Tt[Tt.length-U.length].length-U[0].length:this.yylloc.first_column-pt},this.options.ranges&&(this.yylloc.range=[nt[0],nt[0]+this.yyleng-pt]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){if(this.options.backtrack_lexer)this._backtrack=!0;else return this.parseError("Lexical error on line "+(this.yylineno+1)+`. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true). +`+this.showPosition(),{text:"",token:null,line:this.yylineno});return this},less:function(X){this.unput(this.match.slice(X))},pastInput:function(){var X=this.matched.substr(0,this.matched.length-this.match.length);return(X.length>20?"...":"")+X.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var X=this.match;return X.length<20&&(X+=this._input.substr(0,20-X.length)),(X.substr(0,20)+(X.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var X=this.pastInput(),pt=new Array(X.length+1).join("-");return X+this.upcomingInput()+` +`+pt+"^"},test_match:function(X,pt){var U,Tt,nt;if(this.options.backtrack_lexer&&(nt={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(nt.yylloc.range=this.yylloc.range.slice(0))),Tt=X[0].match(/(?:\r\n?|\n).*/g),Tt&&(this.yylineno+=Tt.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:Tt?Tt[Tt.length-1].length-Tt[Tt.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+X[0].length},this.yytext+=X[0],this.match+=X[0],this.matches=X,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(X[0].length),this.matched+=X[0],U=this.performAction.call(this,this.yy,this,pt,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),U)return U;if(this._backtrack){for(var It in nt)this[It]=nt[It];return!1}return!1},next:function(){if(this.done)return this.EOF;this._input||(this.done=!0);var X,pt,U,Tt;this._more||(this.yytext="",this.match="");for(var nt=this._currentRules(),It=0;Itpt[0].length)){if(pt=U,Tt=It,this.options.backtrack_lexer){if(X=this.test_match(U,nt[It]),X!==!1)return X;if(this._backtrack){pt=!1;continue}else return!1}else if(!this.options.flex)break}return pt?(X=this.test_match(pt,nt[Tt]),X!==!1?X:!1):this._input===""?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+`. Unrecognized text. +`+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){var pt=this.next();return pt||this.lex()},begin:function(pt){this.conditionStack.push(pt)},popState:function(){var pt=this.conditionStack.length-1;return pt>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(pt){return pt=this.conditionStack.length-1-Math.abs(pt||0),pt>=0?this.conditionStack[pt]:"INITIAL"},pushState:function(pt){this.begin(pt)},stateStackSize:function(){return this.conditionStack.length},options:{"case-insensitive":!0},performAction:function(pt,U,Tt,nt){switch(Tt){case 0:return this.begin("acc_title"),22;case 1:return this.popState(),"acc_title_value";case 2:return this.begin("acc_descr"),24;case 3:return this.popState(),"acc_descr_value";case 4:this.begin("acc_descr_multiline");break;case 5:this.popState();break;case 6:return"acc_descr_multiline_value";case 7:return 10;case 8:break;case 9:return 8;case 10:return 28;case 11:return 48;case 12:return 4;case 13:return this.begin("block"),15;case 14:return 36;case 15:break;case 16:return 37;case 17:return 34;case 18:return 34;case 19:return 38;case 20:break;case 21:return this.popState(),17;case 22:return U.yytext[0];case 23:return 18;case 24:return 19;case 25:return 41;case 26:return 43;case 27:return 43;case 28:return 43;case 29:return 41;case 30:return 41;case 31:return 42;case 32:return 42;case 33:return 42;case 34:return 42;case 35:return 42;case 36:return 43;case 37:return 42;case 38:return 43;case 39:return 44;case 40:return 44;case 41:return 44;case 42:return 44;case 43:return 41;case 44:return 42;case 45:return 43;case 46:return 45;case 47:return 46;case 48:return 47;case 49:return 47;case 50:return 46;case 51:return 46;case 52:return 46;case 53:return 27;case 54:return U.yytext[0];case 55:return 6}},rules:[/^(?:accTitle\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*\{\s*)/i,/^(?:[\}])/i,/^(?:[^\}]*)/i,/^(?:[\n]+)/i,/^(?:\s+)/i,/^(?:[\s]+)/i,/^(?:"[^"%\r\n\v\b\\]+")/i,/^(?:"[^"]*")/i,/^(?:erDiagram\b)/i,/^(?:\{)/i,/^(?:,)/i,/^(?:\s+)/i,/^(?:\b((?:PK)|(?:FK)|(?:UK))\b)/i,/^(?:(.*?)[~](.*?)*[~])/i,/^(?:[\*A-Za-z_][A-Za-z0-9\-_\[\]\(\)]*)/i,/^(?:"[^"]*")/i,/^(?:[\n]+)/i,/^(?:\})/i,/^(?:.)/i,/^(?:\[)/i,/^(?:\])/i,/^(?:one or zero\b)/i,/^(?:one or more\b)/i,/^(?:one or many\b)/i,/^(?:1\+)/i,/^(?:\|o\b)/i,/^(?:zero or one\b)/i,/^(?:zero or more\b)/i,/^(?:zero or many\b)/i,/^(?:0\+)/i,/^(?:\}o\b)/i,/^(?:many\(0\))/i,/^(?:many\(1\))/i,/^(?:many\b)/i,/^(?:\}\|)/i,/^(?:one\b)/i,/^(?:only one\b)/i,/^(?:1\b)/i,/^(?:\|\|)/i,/^(?:o\|)/i,/^(?:o\{)/i,/^(?:\|\{)/i,/^(?:\s*u\b)/i,/^(?:\.\.)/i,/^(?:--)/i,/^(?:to\b)/i,/^(?:optionally to\b)/i,/^(?:\.-)/i,/^(?:-\.)/i,/^(?:[A-Za-z_][A-Za-z0-9\-_]*)/i,/^(?:.)/i,/^(?:$)/i],conditions:{acc_descr_multiline:{rules:[5,6],inclusive:!1},acc_descr:{rules:[3],inclusive:!1},acc_title:{rules:[1],inclusive:!1},block:{rules:[14,15,16,17,18,19,20,21,22],inclusive:!1},INITIAL:{rules:[0,2,4,7,8,9,10,11,12,13,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55],inclusive:!0}}};return vt}();yt.lexer=ft;function ut(){this.yy={}}return ut.prototype=yt,yt.Parser=ut,new ut}();R0t.parser=R0t;const lze=R0t;let mk={},j0t=[];const hze={ZERO_OR_ONE:"ZERO_OR_ONE",ZERO_OR_MORE:"ZERO_OR_MORE",ONE_OR_MORE:"ONE_OR_MORE",ONLY_ONE:"ONLY_ONE",MD_PARENT:"MD_PARENT"},fze={NON_IDENTIFYING:"NON_IDENTIFYING",IDENTIFYING:"IDENTIFYING"},OBt=function(i,a=void 0){return mk[i]===void 0?(mk[i]={attributes:[],alias:a},Ut.info("Added new entity :",i)):mk[i]&&!mk[i].alias&&a&&(mk[i].alias=a,Ut.info(`Add alias '${a}' to entity 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f;i.append("defs").append("marker").attr("id",fm.MD_PARENT_START).attr("refX",0).attr("refY",7).attr("markerWidth",190).attr("markerHeight",240).attr("orient","auto").append("path").attr("d","M 18,7 L9,13 L1,7 L9,1 Z"),i.append("defs").append("marker").attr("id",fm.MD_PARENT_END).attr("refX",19).attr("refY",7).attr("markerWidth",20).attr("markerHeight",28).attr("orient","auto").append("path").attr("d","M 18,7 L9,13 L1,7 L9,1 Z"),i.append("defs").append("marker").attr("id",fm.ONLY_ONE_START).attr("refX",0).attr("refY",9).attr("markerWidth",18).attr("markerHeight",18).attr("orient","auto").append("path").attr("stroke",a.stroke).attr("fill","none").attr("d","M9,0 L9,18 M15,0 L15,18"),i.append("defs").append("marker").attr("id",fm.ONLY_ONE_END).attr("refX",18).attr("refY",9).attr("markerWidth",18).attr("markerHeight",18).attr("orient","auto").append("path").attr("stroke",a.stroke).attr("fill","none").attr("d","M3,0 L3,18 M9,0 L9,18"),f=i.append("defs").append("marker").attr("id",fm.ZERO_OR_ONE_START).attr("refX",0).attr("refY",9).attr("markerWidth",30).attr("markerHeight",18).attr("orient","auto"),f.append("circle").attr("stroke",a.stroke).attr("fill","white").attr("cx",21).attr("cy",9).attr("r",6),f.append("path").attr("stroke",a.stroke).attr("fill","none").attr("d","M9,0 L9,18"),f=i.append("defs").append("marker").attr("id",fm.ZERO_OR_ONE_END).attr("refX",30).attr("refY",9).attr("markerWidth",30).attr("markerHeight",18).attr("orient","auto"),f.append("circle").attr("stroke",a.stroke).attr("fill","white").attr("cx",9).attr("cy",9).attr("r",6),f.append("path").attr("stroke",a.stroke).attr("fill","none").attr("d","M21,0 L21,18"),i.append("defs").append("marker").attr("id",fm.ONE_OR_MORE_START).attr("refX",18).attr("refY",18).attr("markerWidth",45).attr("markerHeight",36).attr("orient","auto").append("path").attr("stroke",a.stroke).attr("fill","none").attr("d","M0,18 Q 18,0 36,18 Q 18,36 0,18 M42,9 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51:return"INVALID"}},rules:[/^(?:%%\{)/i,/^(?:accTitle\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*\{\s*)/i,/^(?:[\}])/i,/^(?:[^\}]*)/i,/^(?:%%(?!\{)*[^\n]*)/i,/^(?:[^\}]%%*[^\n]*)/i,/^(?:%%*[^\n]*[\n]*)/i,/^(?:[\n]+)/i,/^(?:\s+)/i,/^(?:#[^\n]*)/i,/^(?:%[^\n]*)/i,/^(?:href[\s]+["])/i,/^(?:["])/i,/^(?:[^"]*)/i,/^(?:call[\s]+)/i,/^(?:\([\s]*\))/i,/^(?:\()/i,/^(?:[^(]*)/i,/^(?:\))/i,/^(?:[^)]*)/i,/^(?:click[\s]+)/i,/^(?:[\s\n])/i,/^(?:[^\s\n]*)/i,/^(?:gantt\b)/i,/^(?:dateFormat\s[^#\n;]+)/i,/^(?:inclusiveEndDates\b)/i,/^(?:topAxis\b)/i,/^(?:axisFormat\s[^#\n;]+)/i,/^(?:tickInterval\s[^#\n;]+)/i,/^(?:includes\s[^#\n;]+)/i,/^(?:excludes\s[^#\n;]+)/i,/^(?:todayMarker\s[^\n;]+)/i,/^(?:weekday\s+monday\b)/i,/^(?:weekday\s+tuesday\b)/i,/^(?:weekday\s+wednesday\b)/i,/^(?:weekday\s+thursday\b)/i,/^(?:weekday\s+friday\b)/i,/^(?:weekday\s+saturday\b)/i,/^(?:weekday\s+sunday\b)/i,/^(?:\d\d\d\d-\d\d-\d\d\b)/i,/^(?:title\s[^#\n;]+)/i,/^(?:accDescription\s[^#\n;]+)/i,/^(?:section\s[^#:\n;]+)/i,/^(?:[^#:\n;]+)/i,/^(?::[^#\n;]+)/i,/^(?::)/i,/^(?:$)/i,/^(?:.)/i],conditions:{acc_descr_multiline:{rules:[6,7],inclusive:!1},acc_descr:{rules:[4],inclusive:!1},acc_title:{rules:[2],inclusive:!1},callbackargs:{rules:[22,23],inclusive:!1},callbackname:{rules:[19,20,21],inclusive:!1},href:{rules:[16,17],inclusive:!1},click:{rules:[25,26],inclusive:!1},INITIAL:{rules:[0,1,3,5,8,9,10,11,12,13,14,15,18,24,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51],inclusive:!0}}};return 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et,st;et=W,st=E&&E.formats;for(var at=(W=et.replace(/(\[[^\]]+])|(LTS?|l{1,4}|L{1,4})/g,function(X,pt,U){var Tt=U&&U.toUpperCase();return pt||st[U]||f[U]||st[Tt].replace(/(\[[^\]]+])|(MMMM|MM|DD|dddd)/g,function(nt,It,Ot){return It||Ot.slice(1)})})).match(p),bt=at.length,mt=0;mt-1)return new Date((Et==="X"?1e3:1)*Bt);var Ct=z(Et)(Bt),xt=Ct.year,Ht=Ct.month,Le=Ct.day,Ft=Ct.hours,gn=Ct.minutes,Se=Ct.seconds,me=Ct.milliseconds,Ve=Ct.zone,Ye=new Date,ce=Le||(xt||Ht?1:Ye.getDate()),ke=xt||Ye.getFullYear(),zt=0;xt&&!Ht||(zt=Ht>0?Ht-1:Ye.getMonth());var re=Ft||0,se=gn||0,Pe=Se||0,te=me||0;return Ve?new Date(Date.UTC(ke,zt,ce,re,se,Pe,te+60*Ve.offset*1e3)):Z?new Date(Date.UTC(ke,zt,ce,re,se,Pe,te)):new Date(ke,zt,ce,re,se,Pe,te)}catch{return new Date("")}}(yt,vt,ft),this.init(),Tt&&Tt!==!0&&(this.$L=this.locale(Tt).$L),U&&yt!=this.format(vt)&&(this.$d=new Date("")),E={}}else if(vt instanceof Array)for(var nt=vt.length,It=1;It<=nt;It+=1){ut[1]=vt[It-1];var 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0||FtEt)&&(Et=gn);if(!Bt||!Et)return;if(w0(Et).diff(w0(Bt),"year")>5){Ut.warn("The difference between the min and max time is more than 5 years. 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+ font-family: var(--mermaid-font-family); + } + .exclude-range { + fill: ${i.excludeBkgColor}; + } + + .section { + stroke: none; + opacity: 0.2; + } + + .section0 { + fill: ${i.sectionBkgColor}; + } + + .section2 { + fill: ${i.sectionBkgColor2}; + } + + .section1, + .section3 { + fill: ${i.altSectionBkgColor}; + opacity: 0.2; + } + + .sectionTitle0 { + fill: ${i.titleColor}; + } + + .sectionTitle1 { + fill: ${i.titleColor}; + } + + .sectionTitle2 { + fill: ${i.titleColor}; + } + + .sectionTitle3 { + fill: ${i.titleColor}; + } + + .sectionTitle { + text-anchor: start; + // font-size: ${i.ganttFontSize}; + // text-height: 14px; + font-family: 'trebuchet ms', verdana, arial, sans-serif; + font-family: var(--mermaid-font-family); + + } + + + /* Grid and axis */ + + .grid .tick { + stroke: ${i.gridColor}; + opacity: 0.8; + shape-rendering: crispEdges; + text { + font-family: ${i.fontFamily}; + fill: ${i.textColor}; + } + } + + .grid path { + stroke-width: 0; + } + + + /* Today line */ + + .today { + fill: none; + stroke: ${i.todayLineColor}; + stroke-width: 2px; + } + + + /* Task styling */ + + /* Default task */ + + .task { + stroke-width: 2; + } + + .taskText { + text-anchor: middle; + font-family: 'trebuchet ms', verdana, arial, sans-serif; + font-family: var(--mermaid-font-family); + } + + // .taskText:not([font-size]) { + // font-size: ${i.ganttFontSize}; + // } + + .taskTextOutsideRight { + fill: ${i.taskTextDarkColor}; + text-anchor: start; + // font-size: ${i.ganttFontSize}; + font-family: 'trebuchet ms', verdana, arial, sans-serif; + font-family: var(--mermaid-font-family); + + } + + .taskTextOutsideLeft { + fill: ${i.taskTextDarkColor}; + text-anchor: end; + // font-size: ${i.ganttFontSize}; + } + + /* Special case clickable */ + .task.clickable { + cursor: pointer; + } + .taskText.clickable { + cursor: pointer; + fill: ${i.taskTextClickableColor} !important; + font-weight: bold; + } + + .taskTextOutsideLeft.clickable { + cursor: pointer; + fill: ${i.taskTextClickableColor} !important; + font-weight: bold; + } + + .taskTextOutsideRight.clickable { + cursor: pointer; + fill: ${i.taskTextClickableColor} !important; + font-weight: bold; + } + + /* Specific task settings for the sections*/ + + .taskText0, + .taskText1, + .taskText2, + .taskText3 { + fill: ${i.taskTextColor}; + } + + .task0, + .task1, + .task2, + .task3 { + fill: ${i.taskBkgColor}; + stroke: ${i.taskBorderColor}; + } + + .taskTextOutside0, + .taskTextOutside2 + { + fill: ${i.taskTextOutsideColor}; + } + + .taskTextOutside1, + .taskTextOutside3 { + fill: ${i.taskTextOutsideColor}; + } + + + /* Active task */ + + .active0, + .active1, + .active2, + .active3 { + fill: ${i.activeTaskBkgColor}; + stroke: ${i.activeTaskBorderColor}; + } + + .activeText0, + .activeText1, + .activeText2, + .activeText3 { + fill: ${i.taskTextDarkColor} !important; + } + + + /* Completed task */ + + .done0, + .done1, + .done2, + .done3 { + stroke: ${i.doneTaskBorderColor}; + fill: ${i.doneTaskBkgColor}; + stroke-width: 2; + } + + .doneText0, + .doneText1, + .doneText2, + .doneText3 { + fill: ${i.taskTextDarkColor} !important; + } + + + /* Tasks on the critical line */ + + .crit0, + .crit1, + .crit2, + .crit3 { + stroke: ${i.critBorderColor}; + fill: ${i.critBkgColor}; + stroke-width: 2; + } + + .activeCrit0, + .activeCrit1, + .activeCrit2, + .activeCrit3 { + stroke: ${i.critBorderColor}; + fill: ${i.activeTaskBkgColor}; + stroke-width: 2; + } + + .doneCrit0, + .doneCrit1, + .doneCrit2, + .doneCrit3 { + stroke: ${i.critBorderColor}; + fill: ${i.doneTaskBkgColor}; + stroke-width: 2; + cursor: pointer; + shape-rendering: crispEdges; + } + + .milestone { + transform: rotate(45deg) scale(0.8,0.8); + } + + .milestoneText { + font-style: italic; + } + .doneCritText0, + .doneCritText1, + .doneCritText2, + .doneCritText3 { + fill: ${i.taskTextDarkColor} !important; + } + + .activeCritText0, + .activeCritText1, + .activeCritText2, + .activeCritText3 { + fill: ${i.taskTextDarkColor} !important; + } + + .titleText { + text-anchor: middle; + font-size: 18px; + fill: ${i.textColor} ; + font-family: 'trebuchet ms', verdana, arial, sans-serif; + font-family: var(--mermaid-font-family); + } +`}},Symbol.toStringTag,{value:"Module"}));var ngt=function(){var i=function(m,b,E,_){for(E=E||{},_=m.length;_--;E[m[_]]=b);return E},a=[6,9,10],f={trace:function(){},yy:{},symbols_:{error:2,start:3,info:4,document:5,EOF:6,line:7,statement:8,NL:9,showInfo:10,$accept:0,$end:1},terminals_:{2:"error",4:"info",6:"EOF",9:"NL",10:"showInfo"},productions_:[0,[3,3],[5,0],[5,2],[7,1],[7,1],[8,1]],performAction:function(b,E,_,A,I,B,N){switch(B.length-1,I){case 1:return A;case 4:break;case 6:A.setInfo(!0);break}},table:[{3:1,4:[1,2]},{1:[3]},i(a,[2,2],{5:3}),{6:[1,4],7:5,8:6,9:[1,7],10:[1,8]},{1:[2,1]},i(a,[2,3]),i(a,[2,4]),i(a,[2,5]),i(a,[2,6])],defaultActions:{4:[2,1]},parseError:function(b,E){if(E.recoverable)this.trace(b);else{var _=new Error(b);throw _.hash=E,_}},parse:function(b){var E=this,_=[0],A=[],I=[null],B=[],N=this.table,R="",z=0,W=0,et=2,st=1,at=B.slice.call(arguments,1),bt=Object.create(this.lexer),mt={yy:{}};for(var yt in this.yy)Object.prototype.hasOwnProperty.call(this.yy,yt)&&(mt.yy[yt]=this.yy[yt]);bt.setInput(b,mt.yy),mt.yy.lexer=bt,mt.yy.parser=this,typeof bt.yylloc>"u"&&(bt.yylloc={});var ft=bt.yylloc;B.push(ft);var ut=bt.options&&bt.options.ranges;typeof mt.yy.parseError=="function"?this.parseError=mt.yy.parseError:this.parseError=Object.getPrototypeOf(this).parseError;function vt(){var Ct;return Ct=A.pop()||bt.lex()||st,typeof Ct!="number"&&(Ct instanceof Array&&(A=Ct,Ct=A.pop()),Ct=E.symbols_[Ct]||Ct),Ct}for(var X,pt,U,Tt,nt={},It,Ot,Bt,Et;;){if(pt=_[_.length-1],this.defaultActions[pt]?U=this.defaultActions[pt]:((X===null||typeof X>"u")&&(X=vt()),U=N[pt]&&N[pt][X]),typeof U>"u"||!U.length||!U[0]){var Z="";Et=[];for(It in N[pt])this.terminals_[It]&&It>et&&Et.push("'"+this.terminals_[It]+"'");bt.showPosition?Z="Parse error on line "+(z+1)+`: +`+bt.showPosition()+` +Expecting `+Et.join(", ")+", got '"+(this.terminals_[X]||X)+"'":Z="Parse error on line "+(z+1)+": Unexpected "+(X==st?"end of input":"'"+(this.terminals_[X]||X)+"'"),this.parseError(Z,{text:bt.match,token:this.terminals_[X]||X,line:bt.yylineno,loc:ft,expected:Et})}if(U[0]instanceof Array&&U.length>1)throw new Error("Parse Error: multiple actions possible at state: "+pt+", token: "+X);switch(U[0]){case 1:_.push(X),I.push(bt.yytext),B.push(bt.yylloc),_.push(U[1]),X=null,W=bt.yyleng,R=bt.yytext,z=bt.yylineno,ft=bt.yylloc;break;case 2:if(Ot=this.productions_[U[1]][1],nt.$=I[I.length-Ot],nt._$={first_line:B[B.length-(Ot||1)].first_line,last_line:B[B.length-1].last_line,first_column:B[B.length-(Ot||1)].first_column,last_column:B[B.length-1].last_column},ut&&(nt._$.range=[B[B.length-(Ot||1)].range[0],B[B.length-1].range[1]]),Tt=this.performAction.apply(nt,[R,W,z,mt.yy,U[1],I,B].concat(at)),typeof Tt<"u")return Tt;Ot&&(_=_.slice(0,-1*Ot*2),I=I.slice(0,-1*Ot),B=B.slice(0,-1*Ot)),_.push(this.productions_[U[1]][0]),I.push(nt.$),B.push(nt._$),Bt=N[_[_.length-2]][_[_.length-1]],_.push(Bt);break;case 3:return!0}}return!0}},p=function(){var m={EOF:1,parseError:function(E,_){if(this.yy.parser)this.yy.parser.parseError(E,_);else throw new Error(E)},setInput:function(b,E){return this.yy=E||this.yy||{},this._input=b,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var b=this._input[0];this.yytext+=b,this.yyleng++,this.offset++,this.match+=b,this.matched+=b;var E=b.match(/(?:\r\n?|\n).*/g);return E?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),b},unput:function(b){var E=b.length,_=b.split(/(?:\r\n?|\n)/g);this._input=b+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-E),this.offset-=E;var A=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),_.length-1&&(this.yylineno-=_.length-1);var I=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:_?(_.length===A.length?this.yylloc.first_column:0)+A[A.length-_.length].length-_[0].length:this.yylloc.first_column-E},this.options.ranges&&(this.yylloc.range=[I[0],I[0]+this.yyleng-E]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){if(this.options.backtrack_lexer)this._backtrack=!0;else return this.parseError("Lexical error on line "+(this.yylineno+1)+`. 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yt},a=[1,3],f=[1,4],p=[1,5],w=[1,6],m=[1,10,12,14,16,18,19,20,21,22],b=[2,4],E=[1,5,10,12,14,16,18,19,20,21,22],_=[20,21,22],A=[2,7],I=[1,12],B=[1,13],N=[1,14],R=[1,15],z=[1,16],W=[1,17],et={trace:function(){},yy:{},symbols_:{error:2,start:3,eol:4,PIE:5,document:6,showData:7,line:8,statement:9,txt:10,value:11,title:12,title_value:13,acc_title:14,acc_title_value:15,acc_descr:16,acc_descr_value:17,acc_descr_multiline_value:18,section:19,NEWLINE:20,";":21,EOF:22,$accept:0,$end:1},terminals_:{2:"error",5:"PIE",7:"showData",10:"txt",11:"value",12:"title",13:"title_value",14:"acc_title",15:"acc_title_value",16:"acc_descr",17:"acc_descr_value",18:"acc_descr_multiline_value",19:"section",20:"NEWLINE",21:";",22:"EOF"},productions_:[0,[3,2],[3,2],[3,3],[6,0],[6,2],[8,2],[9,0],[9,2],[9,2],[9,2],[9,2],[9,1],[9,1],[4,1],[4,1],[4,1]],performAction:function(mt,yt,ft,ut,vt,X,pt){var U=X.length-1;switch(vt){case 3:ut.setShowData(!0);break;case 6:this.$=X[U-1];break;case 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yt=this,ft=[0],ut=[],vt=[null],X=[],pt=this.table,U="",Tt=0,nt=0,It=2,Ot=1,Bt=X.slice.call(arguments,1),Et=Object.create(this.lexer),Z={yy:{}};for(var Ct in this.yy)Object.prototype.hasOwnProperty.call(this.yy,Ct)&&(Z.yy[Ct]=this.yy[Ct]);Et.setInput(mt,Z.yy),Z.yy.lexer=Et,Z.yy.parser=this,typeof Et.yylloc>"u"&&(Et.yylloc={});var xt=Et.yylloc;X.push(xt);var Ht=Et.options&&Et.options.ranges;typeof Z.yy.parseError=="function"?this.parseError=Z.yy.parseError:this.parseError=Object.getPrototypeOf(this).parseError;function Le(){var se;return se=ut.pop()||Et.lex()||Ot,typeof se!="number"&&(se instanceof Array&&(ut=se,se=ut.pop()),se=yt.symbols_[se]||se),se}for(var Ft,gn,Se,me,Ve={},Ye,ce,ke,zt;;){if(gn=ft[ft.length-1],this.defaultActions[gn]?Se=this.defaultActions[gn]:((Ft===null||typeof Ft>"u")&&(Ft=Le()),Se=pt[gn]&&pt[gn][Ft]),typeof Se>"u"||!Se.length||!Se[0]){var re="";zt=[];for(Ye in pt[gn])this.terminals_[Ye]&&Ye>It&&zt.push("'"+this.terminals_[Ye]+"'");Et.showPosition?re="Parse error on line "+(Tt+1)+`: +`+Et.showPosition()+` +Expecting `+zt.join(", ")+", got '"+(this.terminals_[Ft]||Ft)+"'":re="Parse error on line "+(Tt+1)+": Unexpected "+(Ft==Ot?"end of input":"'"+(this.terminals_[Ft]||Ft)+"'"),this.parseError(re,{text:Et.match,token:this.terminals_[Ft]||Ft,line:Et.yylineno,loc:xt,expected:zt})}if(Se[0]instanceof Array&&Se.length>1)throw new Error("Parse Error: multiple actions possible at state: "+gn+", token: "+Ft);switch(Se[0]){case 1:ft.push(Ft),vt.push(Et.yytext),X.push(Et.yylloc),ft.push(Se[1]),Ft=null,nt=Et.yyleng,U=Et.yytext,Tt=Et.yylineno,xt=Et.yylloc;break;case 2:if(ce=this.productions_[Se[1]][1],Ve.$=vt[vt.length-ce],Ve._$={first_line:X[X.length-(ce||1)].first_line,last_line:X[X.length-1].last_line,first_column:X[X.length-(ce||1)].first_column,last_column:X[X.length-1].last_column},Ht&&(Ve._$.range=[X[X.length-(ce||1)].range[0],X[X.length-1].range[1]]),me=this.performAction.apply(Ve,[U,nt,Tt,Z.yy,Se[1],vt,X].concat(Bt)),typeof me<"u")return me;ce&&(ft=ft.slice(0,-1*ce*2),vt=vt.slice(0,-1*ce),X=X.slice(0,-1*ce)),ft.push(this.productions_[Se[1]][0]),vt.push(Ve.$),X.push(Ve._$),ke=pt[ft[ft.length-2]][ft[ft.length-1]],ft.push(ke);break;case 3:return!0}}return!0}},st=function(){var bt={EOF:1,parseError:function(yt,ft){if(this.yy.parser)this.yy.parser.parseError(yt,ft);else throw new Error(yt)},setInput:function(mt,yt){return this.yy=yt||this.yy||{},this._input=mt,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var mt=this._input[0];this.yytext+=mt,this.yyleng++,this.offset++,this.match+=mt,this.matched+=mt;var yt=mt.match(/(?:\r\n?|\n).*/g);return yt?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),mt},unput:function(mt){var yt=mt.length,ft=mt.split(/(?:\r\n?|\n)/g);this._input=mt+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-yt),this.offset-=yt;var ut=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),ft.length-1&&(this.yylineno-=ft.length-1);var vt=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:ft?(ft.length===ut.length?this.yylloc.first_column:0)+ut[ut.length-ft.length].length-ft[0].length:this.yylloc.first_column-yt},this.options.ranges&&(this.yylloc.range=[vt[0],vt[0]+this.yyleng-yt]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){if(this.options.backtrack_lexer)this._backtrack=!0;else return this.parseError("Lexical error on line "+(this.yylineno+1)+`. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true). +`+this.showPosition(),{text:"",token:null,line:this.yylineno});return this},less:function(mt){this.unput(this.match.slice(mt))},pastInput:function(){var mt=this.matched.substr(0,this.matched.length-this.match.length);return(mt.length>20?"...":"")+mt.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var mt=this.match;return mt.length<20&&(mt+=this._input.substr(0,20-mt.length)),(mt.substr(0,20)+(mt.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var mt=this.pastInput(),yt=new Array(mt.length+1).join("-");return mt+this.upcomingInput()+` +`+yt+"^"},test_match:function(mt,yt){var ft,ut,vt;if(this.options.backtrack_lexer&&(vt={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(vt.yylloc.range=this.yylloc.range.slice(0))),ut=mt[0].match(/(?:\r\n?|\n).*/g),ut&&(this.yylineno+=ut.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:ut?ut[ut.length-1].length-ut[ut.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+mt[0].length},this.yytext+=mt[0],this.match+=mt[0],this.matches=mt,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(mt[0].length),this.matched+=mt[0],ft=this.performAction.call(this,this.yy,this,yt,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),ft)return ft;if(this._backtrack){for(var X in vt)this[X]=vt[X];return!1}return!1},next:function(){if(this.done)return this.EOF;this._input||(this.done=!0);var mt,yt,ft,ut;this._more||(this.yytext="",this.match="");for(var vt=this._currentRules(),X=0;Xyt[0].length)){if(yt=ft,ut=X,this.options.backtrack_lexer){if(mt=this.test_match(ft,vt[X]),mt!==!1)return mt;if(this._backtrack){yt=!1;continue}else return!1}else if(!this.options.flex)break}return yt?(mt=this.test_match(yt,vt[ut]),mt!==!1?mt:!1):this._input===""?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+`. 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this.yy=Ve||this.yy||{},this._input=me,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var me=this._input[0];this.yytext+=me,this.yyleng++,this.offset++,this.match+=me,this.matched+=me;var Ve=me.match(/(?:\r\n?|\n).*/g);return Ve?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),me},unput:function(me){var Ve=me.length,Ye=me.split(/(?:\r\n?|\n)/g);this._input=me+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-Ve),this.offset-=Ve;var ce=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),Ye.length-1&&(this.yylineno-=Ye.length-1);var ke=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:Ye?(Ye.length===ce.length?this.yylloc.first_column:0)+ce[ce.length-Ye.length].length-Ye[0].length:this.yylloc.first_column-Ve},this.options.ranges&&(this.yylloc.range=[ke[0],ke[0]+this.yyleng-Ve]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){if(this.options.backtrack_lexer)this._backtrack=!0;else return this.parseError("Lexical error on line "+(this.yylineno+1)+`. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true). +`+this.showPosition(),{text:"",token:null,line:this.yylineno});return this},less:function(me){this.unput(this.match.slice(me))},pastInput:function(){var me=this.matched.substr(0,this.matched.length-this.match.length);return(me.length>20?"...":"")+me.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var me=this.match;return me.length<20&&(me+=this._input.substr(0,20-me.length)),(me.substr(0,20)+(me.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var me=this.pastInput(),Ve=new Array(me.length+1).join("-");return me+this.upcomingInput()+` +`+Ve+"^"},test_match:function(me,Ve){var Ye,ce,ke;if(this.options.backtrack_lexer&&(ke={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(ke.yylloc.range=this.yylloc.range.slice(0))),ce=me[0].match(/(?:\r\n?|\n).*/g),ce&&(this.yylineno+=ce.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:ce?ce[ce.length-1].length-ce[ce.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+me[0].length},this.yytext+=me[0],this.match+=me[0],this.matches=me,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(me[0].length),this.matched+=me[0],Ye=this.performAction.call(this,this.yy,this,Ve,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),Ye)return Ye;if(this._backtrack){for(var zt in ke)this[zt]=ke[zt];return!1}return!1},next:function(){if(this.done)return this.EOF;this._input||(this.done=!0);var me,Ve,Ye,ce;this._more||(this.yytext="",this.match="");for(var ke=this._currentRules(),zt=0;ztVe[0].length)){if(Ve=Ye,ce=zt,this.options.backtrack_lexer){if(me=this.test_match(Ye,ke[zt]),me!==!1)return me;if(this._backtrack){Ve=!1;continue}else return!1}else if(!this.options.flex)break}return Ve?(me=this.test_match(Ve,ke[ce]),me!==!1?me:!1):this._input===""?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+`. Unrecognized text. +`+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){var Ve=this.next();return Ve||this.lex()},begin:function(Ve){this.conditionStack.push(Ve)},popState:function(){var Ve=this.conditionStack.length-1;return Ve>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(Ve){return Ve=this.conditionStack.length-1-Math.abs(Ve||0),Ve>=0?this.conditionStack[Ve]:"INITIAL"},pushState:function(Ve){this.begin(Ve)},stateStackSize:function(){return this.conditionStack.length},options:{"case-insensitive":!0},performAction:function(Ve,Ye,ce,ke){switch(ce){case 0:break;case 1:break;case 2:return 32;case 3:break;case 4:return this.begin("title"),13;case 5:return this.popState(),"title_value";case 6:return this.begin("acc_title"),15;case 7:return this.popState(),"acc_title_value";case 8:return this.begin("acc_descr"),17;case 9:return this.popState(),"acc_descr_value";case 10:this.begin("acc_descr_multiline");break;case 11:this.popState();break;case 12:return"acc_descr_multiline_value";case 13:return 25;case 14:return 27;case 15:return 26;case 16:return 28;case 17:return 29;case 18:return 30;case 19:return 31;case 20:this.begin("md_string");break;case 21:return"MD_STR";case 22:this.popState();break;case 23:this.begin("string");break;case 24:this.popState();break;case 25:return"STR";case 26:return this.begin("point_start"),22;case 27:return this.begin("point_x"),23;case 28:this.popState();break;case 29:this.popState(),this.begin("point_y");break;case 30:return this.popState(),24;case 31:return 6;case 32:return 43;case 33:return"COLON";case 34:return 45;case 35:return 44;case 36:return 46;case 37:return 46;case 38:return 47;case 39:return 49;case 40:return 50;case 41:return 48;case 42:return 41;case 43:return 51;case 44:return 42;case 45:return 5;case 46:return 33;case 47:return 40;case 48:return 34}},rules:[/^(?:%%(?!\{)[^\n]*)/i,/^(?:[^\}]%%[^\n]*)/i,/^(?:[\n\r]+)/i,/^(?:%%[^\n]*)/i,/^(?:title\b)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accTitle\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*\{\s*)/i,/^(?:[\}])/i,/^(?:[^\}]*)/i,/^(?: *x-axis *)/i,/^(?: *y-axis *)/i,/^(?: *--+> *)/i,/^(?: *quadrant-1 *)/i,/^(?: *quadrant-2 *)/i,/^(?: *quadrant-3 *)/i,/^(?: *quadrant-4 *)/i,/^(?:["][`])/i,/^(?:[^`"]+)/i,/^(?:[`]["])/i,/^(?:["])/i,/^(?:["])/i,/^(?:[^"]*)/i,/^(?:\s*:\s*\[\s*)/i,/^(?:(1)|(0(.\d+)?))/i,/^(?:\s*\] *)/i,/^(?:\s*,\s*)/i,/^(?:(1)|(0(.\d+)?))/i,/^(?: *quadrantChart *)/i,/^(?:[A-Za-z]+)/i,/^(?::)/i,/^(?:\+)/i,/^(?:,)/i,/^(?:=)/i,/^(?:=)/i,/^(?:\*)/i,/^(?:#)/i,/^(?:[\_])/i,/^(?:\.)/i,/^(?:&)/i,/^(?:-)/i,/^(?:[0-9]+)/i,/^(?:\s)/i,/^(?:;)/i,/^(?:[!"#$%&'*+,-.`?\\_/])/i,/^(?:$)/i],conditions:{point_y:{rules:[30],inclusive:!1},point_x:{rules:[29],inclusive:!1},point_start:{rules:[27,28],inclusive:!1},acc_descr_multiline:{rules:[11,12],inclusive:!1},acc_descr:{rules:[9],inclusive:!1},acc_title:{rules:[7],inclusive:!1},title:{rules:[5],inclusive:!1},md_string:{rules:[21,22],inclusive:!1},string:{rules:[24,25],inclusive:!1},INITIAL:{rules:[0,1,2,3,4,6,8,10,13,14,15,16,17,18,19,20,23,26,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48],inclusive:!0}}};return Se}();Le.lexer=Ft;function gn(){this.yy={}}return gn.prototype=Le,Le.Parser=gn,new gn}();agt.parser=agt;const iHe=agt,mg=X1t();class sHe{constructor(){this.config=this.getDefaultConfig(),this.themeConfig=this.getDefaultThemeConfig(),this.data=this.getDefaultData()}getDefaultData(){return{titleText:"",quadrant1Text:"",quadrant2Text:"",quadrant3Text:"",quadrant4Text:"",xAxisLeftText:"",xAxisRightText:"",yAxisBottomText:"",yAxisTopText:"",points:[]}}getDefaultConfig(){var a,f,p,w,m,b,E,_,A,I,B,N,R,z,W,et,st,at;return{showXAxis:!0,showYAxis:!0,showTitle:!0,chartHeight:((a=Zh.quadrantChart)==null?void 0:a.chartWidth)||500,chartWidth:((f=Zh.quadrantChart)==null?void 0:f.chartHeight)||500,titlePadding:((p=Zh.quadrantChart)==null?void 0:p.titlePadding)||10,titleFontSize:((w=Zh.quadrantChart)==null?void 0:w.titleFontSize)||20,quadrantPadding:((m=Zh.quadrantChart)==null?void 0:m.quadrantPadding)||5,xAxisLabelPadding:((b=Zh.quadrantChart)==null?void 0:b.xAxisLabelPadding)||5,yAxisLabelPadding:((E=Zh.quadrantChart)==null?void 0:E.yAxisLabelPadding)||5,xAxisLabelFontSize:((_=Zh.quadrantChart)==null?void 0:_.xAxisLabelFontSize)||16,yAxisLabelFontSize:((A=Zh.quadrantChart)==null?void 0:A.yAxisLabelFontSize)||16,quadrantLabelFontSize:((I=Zh.quadrantChart)==null?void 0:I.quadrantLabelFontSize)||16,quadrantTextTopPadding:((B=Zh.quadrantChart)==null?void 0:B.quadrantTextTopPadding)||5,pointTextPadding:((N=Zh.quadrantChart)==null?void 0:N.pointTextPadding)||5,pointLabelFontSize:((R=Zh.quadrantChart)==null?void 0:R.pointLabelFontSize)||12,pointRadius:((z=Zh.quadrantChart)==null?void 0:z.pointRadius)||5,xAxisPosition:((W=Zh.quadrantChart)==null?void 0:W.xAxisPosition)||"top",yAxisPosition:((et=Zh.quadrantChart)==null?void 0:et.yAxisPosition)||"left",quadrantInternalBorderStrokeWidth:((st=Zh.quadrantChart)==null?void 0:st.quadrantInternalBorderStrokeWidth)||1,quadrantExternalBorderStrokeWidth:((at=Zh.quadrantChart)==null?void 0:at.quadrantExternalBorderStrokeWidth)||2}}getDefaultThemeConfig(){return{quadrant1Fill:mg.quadrant1Fill,quadrant2Fill:mg.quadrant2Fill,quadrant3Fill:mg.quadrant3Fill,quadrant4Fill:mg.quadrant4Fill,quadrant1TextFill:mg.quadrant1TextFill,quadrant2TextFill:mg.quadrant2TextFill,quadrant3TextFill:mg.quadrant3TextFill,quadrant4TextFill:mg.quadrant4TextFill,quadrantPointFill:mg.quadrantPointFill,quadrantPointTextFill:mg.quadrantPointTextFill,quadrantXAxisTextFill:mg.quadrantXAxisTextFill,quadrantYAxisTextFill:mg.quadrantYAxisTextFill,quadrantTitleFill:mg.quadrantTitleFill,quadrantInternalBorderStrokeFill:mg.quadrantInternalBorderStrokeFill,quadrantExternalBorderStrokeFill:mg.quadrantExternalBorderStrokeFill}}clear(){this.config=this.getDefaultConfig(),this.themeConfig=this.getDefaultThemeConfig(),this.data=this.getDefaultData(),Ut.info("clear called")}setData(a){this.data={...this.data,...a}}addPoints(a){this.data.points=[...a,...this.data.points]}setConfig(a){Ut.trace("setConfig called with: ",a),this.config={...this.config,...a}}setThemeConfig(a){Ut.trace("setThemeConfig called with: ",a),this.themeConfig={...this.themeConfig,...a}}calculateSpace(a,f,p,w){const m=this.config.xAxisLabelPadding*2+this.config.xAxisLabelFontSize,b={top:a==="top"&&f?m:0,bottom:a==="bottom"&&f?m:0},E=this.config.yAxisLabelPadding*2+this.config.yAxisLabelFontSize,_={left:this.config.yAxisPosition==="left"&&p?E:0,right:this.config.yAxisPosition==="right"&&p?E:0},A=this.config.titleFontSize+this.config.titlePadding*2,I={top:w?A:0},B=this.config.quadrantPadding+_.left,N=this.config.quadrantPadding+b.top+I.top,R=this.config.chartWidth-this.config.quadrantPadding*2-_.left-_.right,z=this.config.chartHeight-this.config.quadrantPadding*2-b.top-b.bottom-I.top,W=R/2,et=z/2;return{xAxisSpace:b,yAxisSpace:_,titleSpace:I,quadrantSpace:{quadrantLeft:B,quadrantTop:N,quadrantWidth:R,quadrantHalfWidth:W,quadrantHeight:z,quadrantHalfHeight:et}}}getAxisLabels(a,f,p,w){const{quadrantSpace:m,titleSpace:b}=w,{quadrantHalfHeight:E,quadrantHeight:_,quadrantLeft:A,quadrantHalfWidth:I,quadrantTop:B,quadrantWidth:N}=m,R=!!this.data.xAxisRightText,z=!!this.data.yAxisTopText,W=[];return this.data.xAxisLeftText&&f&&W.push({text:this.data.xAxisLeftText,fill:this.themeConfig.quadrantXAxisTextFill,x:A+(R?I/2:0),y:a==="top"?this.config.xAxisLabelPadding+b.top:this.config.xAxisLabelPadding+B+_+this.config.quadrantPadding,fontSize:this.config.xAxisLabelFontSize,verticalPos:R?"center":"left",horizontalPos:"top",rotation:0}),this.data.xAxisRightText&&f&&W.push({text:this.data.xAxisRightText,fill:this.themeConfig.quadrantXAxisTextFill,x:A+I+(R?I/2:0),y:a==="top"?this.config.xAxisLabelPadding+b.top:this.config.xAxisLabelPadding+B+_+this.config.quadrantPadding,fontSize:this.config.xAxisLabelFontSize,verticalPos:R?"center":"left",horizontalPos:"top",rotation:0}),this.data.yAxisBottomText&&p&&W.push({text:this.data.yAxisBottomText,fill:this.themeConfig.quadrantYAxisTextFill,x:this.config.yAxisPosition==="left"?this.config.yAxisLabelPadding:this.config.yAxisLabelPadding+A+N+this.config.quadrantPadding,y:B+_-(z?E/2:0),fontSize:this.config.yAxisLabelFontSize,verticalPos:z?"center":"left",horizontalPos:"top",rotation:-90}),this.data.yAxisTopText&&p&&W.push({text:this.data.yAxisTopText,fill:this.themeConfig.quadrantYAxisTextFill,x:this.config.yAxisPosition==="left"?this.config.yAxisLabelPadding:this.config.yAxisLabelPadding+A+N+this.config.quadrantPadding,y:B+E-(z?E/2:0),fontSize:this.config.yAxisLabelFontSize,verticalPos:z?"center":"left",horizontalPos:"top",rotation:-90}),W}getQuadrants(a){const{quadrantSpace:f}=a,{quadrantHalfHeight:p,quadrantLeft:w,quadrantHalfWidth:m,quadrantTop:b}=f,E=[{text:{text:this.data.quadrant1Text,fill:this.themeConfig.quadrant1TextFill,x:0,y:0,fontSize:this.config.quadrantLabelFontSize,verticalPos:"center",horizontalPos:"middle",rotation:0},x:w+m,y:b,width:m,height:p,fill:this.themeConfig.quadrant1Fill},{text:{text:this.data.quadrant2Text,fill:this.themeConfig.quadrant2TextFill,x:0,y:0,fontSize:this.config.quadrantLabelFontSize,verticalPos:"center",horizontalPos:"middle",rotation:0},x:w,y:b,width:m,height:p,fill:this.themeConfig.quadrant2Fill},{text:{text:this.data.quadrant3Text,fill:this.themeConfig.quadrant3TextFill,x:0,y:0,fontSize:this.config.quadrantLabelFontSize,verticalPos:"center",horizontalPos:"middle",rotation:0},x:w,y:b+p,width:m,height:p,fill:this.themeConfig.quadrant3Fill},{text:{text:this.data.quadrant4Text,fill:this.themeConfig.quadrant4TextFill,x:0,y:0,fontSize:this.config.quadrantLabelFontSize,verticalPos:"center",horizontalPos:"middle",rotation:0},x:w+m,y:b+p,width:m,height:p,fill:this.themeConfig.quadrant4Fill}];for(const _ of E)_.text.x=_.x+_.width/2,this.data.points.length===0?(_.text.y=_.y+_.height/2,_.text.horizontalPos="middle"):(_.text.y=_.y+this.config.quadrantTextTopPadding,_.text.horizontalPos="top");return E}getQuadrantPoints(a){const{quadrantSpace:f}=a,{quadrantHeight:p,quadrantLeft:w,quadrantTop:m,quadrantWidth:b}=f,E=AA().domain([0,1]).range([w,b+w]),_=AA().domain([0,1]).range([p+m,m]);return this.data.points.map(I=>({x:E(I.x),y:_(I.y),fill:this.themeConfig.quadrantPointFill,radius:this.config.pointRadius,text:{text:I.text,fill:this.themeConfig.quadrantPointTextFill,x:E(I.x),y:_(I.y)+this.config.pointTextPadding,verticalPos:"center",horizontalPos:"top",fontSize:this.config.pointLabelFontSize,rotation:0}}))}getBorders(a){const f=this.config.quadrantExternalBorderStrokeWidth/2,{quadrantSpace:p}=a,{quadrantHalfHeight:w,quadrantHeight:m,quadrantLeft:b,quadrantHalfWidth:E,quadrantTop:_,quadrantWidth:A}=p;return[{strokeFill:this.themeConfig.quadrantExternalBorderStrokeFill,strokeWidth:this.config.quadrantExternalBorderStrokeWidth,x1:b-f,y1:_,x2:b+A+f,y2:_},{strokeFill:this.themeConfig.quadrantExternalBorderStrokeFill,strokeWidth:this.config.quadrantExternalBorderStrokeWidth,x1:b+A,y1:_+f,x2:b+A,y2:_+m-f},{strokeFill:this.themeConfig.quadrantExternalBorderStrokeFill,strokeWidth:this.config.quadrantExternalBorderStrokeWidth,x1:b-f,y1:_+m,x2:b+A+f,y2:_+m},{strokeFill:this.themeConfig.quadrantExternalBorderStrokeFill,strokeWidth:this.config.quadrantExternalBorderStrokeWidth,x1:b,y1:_+f,x2:b,y2:_+m-f},{strokeFill:this.themeConfig.quadrantInternalBorderStrokeFill,strokeWidth:this.config.quadrantInternalBorderStrokeWidth,x1:b+E,y1:_+f,x2:b+E,y2:_+m-f},{strokeFill:this.themeConfig.quadrantInternalBorderStrokeFill,strokeWidth:this.config.quadrantInternalBorderStrokeWidth,x1:b+f,y1:_+w,x2:b+A-f,y2:_+w}]}getTitle(a){if(a)return{text:this.data.titleText,fill:this.themeConfig.quadrantTitleFill,fontSize:this.config.titleFontSize,horizontalPos:"top",verticalPos:"center",rotation:0,y:this.config.titlePadding,x:this.config.chartWidth/2}}build(){const a=this.config.showXAxis&&!!(this.data.xAxisLeftText||this.data.xAxisRightText),f=this.config.showYAxis&&!!(this.data.yAxisTopText||this.data.yAxisBottomText),p=this.config.showTitle&&!!this.data.titleText,w=this.data.points.length>0?"bottom":this.config.xAxisPosition,m=this.calculateSpace(w,a,f,p);return{points:this.getQuadrantPoints(m),quadrants:this.getQuadrants(m),axisLabels:this.getAxisLabels(w,a,f,m),borderLines:this.getBorders(m),title:this.getTitle(p)}}}const aHe=Oe();function B5(i){return Q1(i.trim(),aHe)}const _0=new sHe;function oHe(i){_0.setData({quadrant1Text:B5(i.text)})}function cHe(i){_0.setData({quadrant2Text:B5(i.text)})}function uHe(i){_0.setData({quadrant3Text:B5(i.text)})}function lHe(i){_0.setData({quadrant4Text:B5(i.text)})}function hHe(i){_0.setData({xAxisLeftText:B5(i.text)})}function fHe(i){_0.setData({xAxisRightText:B5(i.text)})}function dHe(i){_0.setData({yAxisTopText:B5(i.text)})}function gHe(i){_0.setData({yAxisBottomText:B5(i.text)})}function pHe(i,a,f){_0.addPoints([{x:a,y:f,text:B5(i.text)}])}function bHe(i){_0.setConfig({chartWidth:i})}function wHe(i){_0.setConfig({chartHeight:i})}function vHe(){const i=Oe(),{themeVariables:a,quadrantChart:f}=i;return f&&_0.setConfig(f),_0.setThemeConfig({quadrant1Fill:a.quadrant1Fill,quadrant2Fill:a.quadrant2Fill,quadrant3Fill:a.quadrant3Fill,quadrant4Fill:a.quadrant4Fill,quadrant1TextFill:a.quadrant1TextFill,quadrant2TextFill:a.quadrant2TextFill,quadrant3TextFill:a.quadrant3TextFill,quadrant4TextFill:a.quadrant4TextFill,quadrantPointFill:a.quadrantPointFill,quadrantPointTextFill:a.quadrantPointTextFill,quadrantXAxisTextFill:a.quadrantXAxisTextFill,quadrantYAxisTextFill:a.quadrantYAxisTextFill,quadrantExternalBorderStrokeFill:a.quadrantExternalBorderStrokeFill,quadrantInternalBorderStrokeFill:a.quadrantInternalBorderStrokeFill,quadrantTitleFill:a.quadrantTitleFill}),_0.setData({titleText:pg()}),_0.build()}const mHe=Object.freeze(Object.defineProperty({__proto__:null,diagram:{parser:iHe,db:{setWidth:bHe,setHeight:wHe,setQuadrant1Text:oHe,setQuadrant2Text:cHe,setQuadrant3Text:uHe,setQuadrant4Text:lHe,setXAxisLeftText:hHe,setXAxisRightText:fHe,setYAxisTopText:dHe,setYAxisBottomText:gHe,addPoint:pHe,getQuadrantData:vHe,clear:function(){_0.clear(),hg()},setAccTitle:E0,getAccTitle:fg,setDiagramTitle:Nb,getDiagramTitle:pg,getAccDescription:gg,setAccDescription:dg},renderer:{draw:(i,a,f,p)=>{var vt,X,pt;function w(U){return U==="top"?"hanging":"middle"}function m(U){return U==="left"?"start":"middle"}function b(U){return`translate(${U.x}, ${U.y}) rotate(${U.rotation||0})`}const E=Oe();Ut.debug(`Rendering quadrant chart +`+i);const _=E.securityLevel;let A;_==="sandbox"&&(A=yr("#i"+a));const B=yr(_==="sandbox"?A.nodes()[0].contentDocument.body:"body").select(`[id="${a}"]`),N=B.append("g").attr("class","main"),R=((vt=E.quadrantChart)==null?void 0:vt.chartWidth)||500,z=((X=E.quadrantChart)==null?void 0:X.chartHeight)||500;k0(B,z,R,((pt=E.quadrantChart)==null?void 0:pt.useMaxWidth)||!0),B.attr("viewBox","0 0 "+R+" "+z),p.db.setHeight(z),p.db.setWidth(R);const W=p.db.getQuadrantData(),et=N.append("g").attr("class","quadrants"),st=N.append("g").attr("class","border"),at=N.append("g").attr("class","data-points"),bt=N.append("g").attr("class","labels"),mt=N.append("g").attr("class","title");W.title&&mt.append("text").attr("x",0).attr("y",0).attr("fill",W.title.fill).attr("font-size",W.title.fontSize).attr("dominant-baseline",w(W.title.horizontalPos)).attr("text-anchor",m(W.title.verticalPos)).attr("transform",b(W.title)).text(W.title.text),W.borderLines&&st.selectAll("line").data(W.borderLines).enter().append("line").attr("x1",U=>U.x1).attr("y1",U=>U.y1).attr("x2",U=>U.x2).attr("y2",U=>U.y2).style("stroke",U=>U.strokeFill).style("stroke-width",U=>U.strokeWidth);const yt=et.selectAll("g.quadrant").data(W.quadrants).enter().append("g").attr("class","quadrant");yt.append("rect").attr("x",U=>U.x).attr("y",U=>U.y).attr("width",U=>U.width).attr("height",U=>U.height).attr("fill",U=>U.fill),yt.append("text").attr("x",0).attr("y",0).attr("fill",U=>U.text.fill).attr("font-size",U=>U.text.fontSize).attr("dominant-baseline",U=>w(U.text.horizontalPos)).attr("text-anchor",U=>m(U.text.verticalPos)).attr("transform",U=>b(U.text)).text(U=>U.text.text),bt.selectAll("g.label").data(W.axisLabels).enter().append("g").attr("class","label").append("text").attr("x",0).attr("y",0).text(U=>U.text).attr("fill",U=>U.fill).attr("font-size",U=>U.fontSize).attr("dominant-baseline",U=>w(U.horizontalPos)).attr("text-anchor",U=>m(U.verticalPos)).attr("transform",U=>b(U));const 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this.pushState("acc_title"),19;case 8:return this.popState(),"acc_title_value";case 9:return this.pushState("acc_descr"),21;case 10:return this.popState(),"acc_descr_value";case 11:this.pushState("acc_descr_multiline");break;case 12:this.popState();break;case 13:return"acc_descr_multiline_value";case 14:return 5;case 15:return 8;case 16:return this.pushState("axis_data"),"X_AXIS";case 17:return this.pushState("axis_data"),"Y_AXIS";case 18:return this.pushState("axis_band_data"),24;case 19:return 31;case 20:return this.pushState("data"),16;case 21:return this.pushState("data"),18;case 22:return this.pushState("data_inner"),24;case 23:return 27;case 24:return this.popState(),26;case 25:this.popState();break;case 26:this.pushState("string");break;case 27:this.popState();break;case 28:return"STR";case 29:return 24;case 30:return 26;case 31:return 43;case 32:return"COLON";case 33:return 44;case 34:return 28;case 35:return 45;case 36:return 46;case 37:return 48;case 38:return 50;case 39:return 47;case 40:return 41;case 41:return 49;case 42:return 42;case 43:break;case 44:return 35;case 45:return 36}},rules:[/^(?:%%(?!\{)[^\n]*)/i,/^(?:[^\}]%%[^\n]*)/i,/^(?:(\r?\n))/i,/^(?:(\r?\n))/i,/^(?:[\n\r]+)/i,/^(?:%%[^\n]*)/i,/^(?:title\b)/i,/^(?:accTitle\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*\{\s*)/i,/^(?:\{)/i,/^(?:[^\}]*)/i,/^(?:xychart-beta\b)/i,/^(?:(?:vertical|horizontal))/i,/^(?:x-axis\b)/i,/^(?:y-axis\b)/i,/^(?:\[)/i,/^(?:-->)/i,/^(?:line\b)/i,/^(?:bar\b)/i,/^(?:\[)/i,/^(?:[+-]?(?:\d+(?:\.\d+)?|\.\d+))/i,/^(?:\])/i,/^(?:(?:`\) \{ this\.pushState\(md_string\); \}\n\(\?:\(\?!`"\)\.\)\+ \{ return MD_STR; \}\n\(\?:`))/i,/^(?:["])/i,/^(?:["])/i,/^(?:[^"]*)/i,/^(?:\[)/i,/^(?:\])/i,/^(?:[A-Za-z]+)/i,/^(?::)/i,/^(?:\+)/i,/^(?:,)/i,/^(?:=)/i,/^(?:\*)/i,/^(?:#)/i,/^(?:[\_])/i,/^(?:\.)/i,/^(?:&)/i,/^(?:-)/i,/^(?:[0-9]+)/i,/^(?:\s+)/i,/^(?:;)/i,/^(?:$)/i],conditions:{data_inner:{rules:[0,1,4,5,6,7,9,11,14,15,16,17,20,21,23,24,25,26,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45],inclusive:!0},data:{rules:[0,1,3,4,5,6,7,9,11,14,15,16,17,20,21,22,25,26,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45],inclusive:!0},axis_band_data:{rules:[0,1,4,5,6,7,9,11,14,15,16,17,20,21,24,25,26,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45],inclusive:!0},axis_data:{rules:[0,1,2,4,5,6,7,9,11,14,15,16,17,18,19,20,21,23,25,26,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45],inclusive:!0},acc_descr_multiline:{rules:[12,13],inclusive:!1},acc_descr:{rules:[10],inclusive:!1},acc_title:{rules:[8],inclusive:!1},title:{rules:[],inclusive:!1},md_string:{rules:[],inclusive:!1},string:{rules:[27,28],inclusive:!1},INITIAL:{rules:[0,1,4,5,6,7,9,11,14,15,16,17,20,21,25,26,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45],inclusive:!0}}};return Ot}();Tt.lexer=nt;function It(){this.yy={}}return It.prototype=Tt,Tt.Parser=It,new It}();ogt.parser=ogt;const yHe=ogt;function oRt(i){return i.type==="bar"}function cRt(i){return i.type==="band"}function BF(i){return i.type==="linear"}class uRt{constructor(a){this.parentGroup=a}getMaxDimension(a,f){if(!this.parentGroup)return{width:a.reduce((m,b)=>Math.max(b.length,m),0)*f,height:f};const p={width:0,height:0},w=this.parentGroup.append("g").attr("visibility","hidden").attr("font-size",f);for(const m of a){const b=k$e(w,1,m),E=b?b.width:m.length*f,_=b?b.height:f;p.width=Math.max(p.width,E),p.height=Math.max(p.height,_)}return w.remove(),p}}const lRt=.7,hRt=.2;class fRt{constructor(a,f,p,w){this.axisConfig=a,this.title=f,this.textDimensionCalculator=p,this.axisThemeConfig=w,this.boundingRect={x:0,y:0,width:0,height:0},this.axisPosition="left",this.showTitle=!1,this.showLabel=!1,this.showTick=!1,this.showAxisLine=!1,this.outerPadding=0,this.titleTextHeight=0,this.labelTextHeight=0,this.range=[0,10],this.boundingRect={x:0,y:0,width:0,height:0},this.axisPosition="left"}setRange(a){this.range=a,this.axisPosition==="left"||this.axisPosition==="right"?this.boundingRect.height=a[1]-a[0]:this.boundingRect.width=a[1]-a[0],this.recalculateScale()}getRange(){return[this.range[0]+this.outerPadding,this.range[1]-this.outerPadding]}setAxisPosition(a){this.axisPosition=a,this.setRange(this.range)}getTickDistance(){const a=this.getRange();return Math.abs(a[0]-a[1])/this.getTickValues().length}getAxisOuterPadding(){return this.outerPadding}getLabelDimension(){return this.textDimensionCalculator.getMaxDimension(this.getTickValues().map(a=>a.toString()),this.axisConfig.labelFontSize)}recalculateOuterPaddingToDrawBar(){lRt*this.getTickDistance()>this.outerPadding*2&&(this.outerPadding=Math.floor(lRt*this.getTickDistance()/2)),this.recalculateScale()}calculateSpaceIfDrawnHorizontally(a){let f=a.height;if(this.axisConfig.showAxisLine&&f>this.axisConfig.axisLineWidth&&(f-=this.axisConfig.axisLineWidth,this.showAxisLine=!0),this.axisConfig.showLabel){const p=this.getLabelDimension(),w=hRt*a.width;this.outerPadding=Math.min(p.width/2,w);const m=p.height+this.axisConfig.labelPadding*2;this.labelTextHeight=p.height,m<=f&&(f-=m,this.showLabel=!0)}if(this.axisConfig.showTick&&f>=this.axisConfig.tickLength&&(this.showTick=!0,f-=this.axisConfig.tickLength),this.axisConfig.showTitle&&this.title){const p=this.textDimensionCalculator.getMaxDimension([this.title],this.axisConfig.titleFontSize),w=p.height+this.axisConfig.titlePadding*2;this.titleTextHeight=p.height,w<=f&&(f-=w,this.showTitle=!0)}this.boundingRect.width=a.width,this.boundingRect.height=a.height-f}calculateSpaceIfDrawnVertical(a){let f=a.width;if(this.axisConfig.showAxisLine&&f>this.axisConfig.axisLineWidth&&(f-=this.axisConfig.axisLineWidth,this.showAxisLine=!0),this.axisConfig.showLabel){const p=this.getLabelDimension(),w=hRt*a.height;this.outerPadding=Math.min(p.height/2,w);const m=p.width+this.axisConfig.labelPadding*2;m<=f&&(f-=m,this.showLabel=!0)}if(this.axisConfig.showTick&&f>=this.axisConfig.tickLength&&(this.showTick=!0,f-=this.axisConfig.tickLength),this.axisConfig.showTitle&&this.title){const p=this.textDimensionCalculator.getMaxDimension([this.title],this.axisConfig.titleFontSize),w=p.height+this.axisConfig.titlePadding*2;this.titleTextHeight=p.height,w<=f&&(f-=w,this.showTitle=!0)}this.boundingRect.width=a.width-f,this.boundingRect.height=a.height}calculateSpace(a){return this.axisPosition==="left"||this.axisPosition==="right"?this.calculateSpaceIfDrawnVertical(a):this.calculateSpaceIfDrawnHorizontally(a),this.recalculateScale(),{width:this.boundingRect.width,height:this.boundingRect.height}}setBoundingBoxXY(a){this.boundingRect.x=a.x,this.boundingRect.y=a.y}getDrawableElementsForLeftAxis(){const a=[];if(this.showAxisLine){const f=this.boundingRect.x+this.boundingRect.width-this.axisConfig.axisLineWidth/2;a.push({type:"path",groupTexts:["left-axis","axisl-line"],data:[{path:`M ${f},${this.boundingRect.y} L ${f},${this.boundingRect.y+this.boundingRect.height} `,strokeFill:this.axisThemeConfig.axisLineColor,strokeWidth:this.axisConfig.axisLineWidth}]})}if(this.showLabel&&a.push({type:"text",groupTexts:["left-axis","label"],data:this.getTickValues().map(f=>({text:f.toString(),x:this.boundingRect.x+this.boundingRect.width-(this.showLabel?this.axisConfig.labelPadding:0)-(this.showTick?this.axisConfig.tickLength:0)-(this.showAxisLine?this.axisConfig.axisLineWidth:0),y:this.getScaleValue(f),fill:this.axisThemeConfig.labelColor,fontSize:this.axisConfig.labelFontSize,rotation:0,verticalPos:"middle",horizontalPos:"right"}))}),this.showTick){const f=this.boundingRect.x+this.boundingRect.width-(this.showAxisLine?this.axisConfig.axisLineWidth:0);a.push({type:"path",groupTexts:["left-axis","ticks"],data:this.getTickValues().map(p=>({path:`M ${f},${this.getScaleValue(p)} L ${f-this.axisConfig.tickLength},${this.getScaleValue(p)}`,strokeFill:this.axisThemeConfig.tickColor,strokeWidth:this.axisConfig.tickWidth}))})}return this.showTitle&&a.push({type:"text",groupTexts:["left-axis","title"],data:[{text:this.title,x:this.boundingRect.x+this.axisConfig.titlePadding,y:this.boundingRect.y+this.boundingRect.height/2,fill:this.axisThemeConfig.titleColor,fontSize:this.axisConfig.titleFontSize,rotation:270,verticalPos:"top",horizontalPos:"center"}]}),a}getDrawableElementsForBottomAxis(){const a=[];if(this.showAxisLine){const f=this.boundingRect.y+this.axisConfig.axisLineWidth/2;a.push({type:"path",groupTexts:["bottom-axis","axis-line"],data:[{path:`M ${this.boundingRect.x},${f} L ${this.boundingRect.x+this.boundingRect.width},${f}`,strokeFill:this.axisThemeConfig.axisLineColor,strokeWidth:this.axisConfig.axisLineWidth}]})}if(this.showLabel&&a.push({type:"text",groupTexts:["bottom-axis","label"],data:this.getTickValues().map(f=>({text:f.toString(),x:this.getScaleValue(f),y:this.boundingRect.y+this.axisConfig.labelPadding+(this.showTick?this.axisConfig.tickLength:0)+(this.showAxisLine?this.axisConfig.axisLineWidth:0),fill:this.axisThemeConfig.labelColor,fontSize:this.axisConfig.labelFontSize,rotation:0,verticalPos:"top",horizontalPos:"center"}))}),this.showTick){const f=this.boundingRect.y+(this.showAxisLine?this.axisConfig.axisLineWidth:0);a.push({type:"path",groupTexts:["bottom-axis","ticks"],data:this.getTickValues().map(p=>({path:`M ${this.getScaleValue(p)},${f} L ${this.getScaleValue(p)},${f+this.axisConfig.tickLength}`,strokeFill:this.axisThemeConfig.tickColor,strokeWidth:this.axisConfig.tickWidth}))})}return this.showTitle&&a.push({type:"text",groupTexts:["bottom-axis","title"],data:[{text:this.title,x:this.range[0]+(this.range[1]-this.range[0])/2,y:this.boundingRect.y+this.boundingRect.height-this.axisConfig.titlePadding-this.titleTextHeight,fill:this.axisThemeConfig.titleColor,fontSize:this.axisConfig.titleFontSize,rotation:0,verticalPos:"top",horizontalPos:"center"}]}),a}getDrawableElementsForTopAxis(){const a=[];if(this.showAxisLine){const f=this.boundingRect.y+this.boundingRect.height-this.axisConfig.axisLineWidth/2;a.push({type:"path",groupTexts:["top-axis","axis-line"],data:[{path:`M ${this.boundingRect.x},${f} L ${this.boundingRect.x+this.boundingRect.width},${f}`,strokeFill:this.axisThemeConfig.axisLineColor,strokeWidth:this.axisConfig.axisLineWidth}]})}if(this.showLabel&&a.push({type:"text",groupTexts:["top-axis","label"],data:this.getTickValues().map(f=>({text:f.toString(),x:this.getScaleValue(f),y:this.boundingRect.y+(this.showTitle?this.titleTextHeight+this.axisConfig.titlePadding*2:0)+this.axisConfig.labelPadding,fill:this.axisThemeConfig.labelColor,fontSize:this.axisConfig.labelFontSize,rotation:0,verticalPos:"top",horizontalPos:"center"}))}),this.showTick){const f=this.boundingRect.y;a.push({type:"path",groupTexts:["top-axis","ticks"],data:this.getTickValues().map(p=>({path:`M ${this.getScaleValue(p)},${f+this.boundingRect.height-(this.showAxisLine?this.axisConfig.axisLineWidth:0)} L ${this.getScaleValue(p)},${f+this.boundingRect.height-this.axisConfig.tickLength-(this.showAxisLine?this.axisConfig.axisLineWidth:0)}`,strokeFill:this.axisThemeConfig.tickColor,strokeWidth:this.axisConfig.tickWidth}))})}return this.showTitle&&a.push({type:"text",groupTexts:["top-axis","title"],data:[{text:this.title,x:this.boundingRect.x+this.boundingRect.width/2,y:this.boundingRect.y+this.axisConfig.titlePadding,fill:this.axisThemeConfig.titleColor,fontSize:this.axisConfig.titleFontSize,rotation:0,verticalPos:"top",horizontalPos:"center"}]}),a}getDrawableElements(){if(this.axisPosition==="left")return this.getDrawableElementsForLeftAxis();if(this.axisPosition==="right")throw Error("Drawing of right axis is not implemented");return this.axisPosition==="bottom"?this.getDrawableElementsForBottomAxis():this.axisPosition==="top"?this.getDrawableElementsForTopAxis():[]}}class xHe extends fRt{constructor(a,f,p,w,m){super(a,w,m,f),this.categories=p,this.scale=S1t().domain(this.categories).range(this.getRange())}setRange(a){super.setRange(a)}recalculateScale(){this.scale=S1t().domain(this.categories).range(this.getRange()).paddingInner(1).paddingOuter(0).align(.5),Ut.trace("BandAxis axis final categories, range: ",this.categories,this.getRange())}getTickValues(){return this.categories}getScaleValue(a){return this.scale(a)||this.getRange()[0]}}class kHe extends fRt{constructor(a,f,p,w,m){super(a,w,m,f),this.domain=p,this.scale=AA().domain(this.domain).range(this.getRange())}getTickValues(){return this.scale.ticks()}recalculateScale(){const a=[...this.domain];this.axisPosition==="left"&&a.reverse(),this.scale=AA().domain(a).range(this.getRange())}getScaleValue(a){return this.scale(a)}}function dRt(i,a,f,p){const w=new uRt(p);return cRt(i)?new xHe(a,f,i.categories,i.title,w):new kHe(a,f,[i.min,i.max],i.title,w)}class EHe{constructor(a,f,p,w){this.textDimensionCalculator=a,this.chartConfig=f,this.chartData=p,this.chartThemeConfig=w,this.boundingRect={x:0,y:0,width:0,height:0},this.showChartTitle=!1}setBoundingBoxXY(a){this.boundingRect.x=a.x,this.boundingRect.y=a.y}calculateSpace(a){const f=this.textDimensionCalculator.getMaxDimension([this.chartData.title],this.chartConfig.titleFontSize),p=Math.max(f.width,a.width),w=f.height+2*this.chartConfig.titlePadding;return f.width<=p&&f.height<=w&&this.chartConfig.showTitle&&this.chartData.title&&(this.boundingRect.width=p,this.boundingRect.height=w,this.showChartTitle=!0),{width:this.boundingRect.width,height:this.boundingRect.height}}getDrawableElements(){const a=[];return this.showChartTitle&&a.push({groupTexts:["chart-title"],type:"text",data:[{fontSize:this.chartConfig.titleFontSize,text:this.chartData.title,verticalPos:"middle",horizontalPos:"center",x:this.boundingRect.x+this.boundingRect.width/2,y:this.boundingRect.y+this.boundingRect.height/2,fill:this.chartThemeConfig.titleColor,rotation:0}]}),a}}function THe(i,a,f,p){const w=new uRt(p);return new EHe(w,i,a,f)}class CHe{constructor(a,f,p,w,m){this.plotData=a,this.xAxis=f,this.yAxis=p,this.orientation=w,this.plotIndex=m}getDrawableElement(){const a=this.plotData.data.map(p=>[this.xAxis.getScaleValue(p[0]),this.yAxis.getScaleValue(p[1])]);let f;return this.orientation==="horizontal"?f=E5().y(p=>p[0]).x(p=>p[1])(a):f=E5().x(p=>p[0]).y(p=>p[1])(a),f?[{groupTexts:["plot",`line-plot-${this.plotIndex}`],type:"path",data:[{path:f,strokeFill:this.plotData.strokeFill,strokeWidth:this.plotData.strokeWidth}]}]:[]}}class _He{constructor(a,f,p,w,m,b){this.barData=a,this.boundingRect=f,this.xAxis=p,this.yAxis=w,this.orientation=m,this.plotIndex=b}getDrawableElement(){const a=this.barData.data.map(m=>[this.xAxis.getScaleValue(m[0]),this.yAxis.getScaleValue(m[1])]),f=.05,p=Math.min(this.xAxis.getAxisOuterPadding()*2,this.xAxis.getTickDistance())*(1-f),w=p/2;return this.orientation==="horizontal"?[{groupTexts:["plot",`bar-plot-${this.plotIndex}`],type:"rect",data:a.map(m=>({x:this.boundingRect.x,y:m[0]-w,height:p,width:m[1]-this.boundingRect.x,fill:this.barData.fill,strokeWidth:0,strokeFill:this.barData.fill}))}]:[{groupTexts:["plot",`bar-plot-${this.plotIndex}`],type:"rect",data:a.map(m=>({x:m[0]-w,y:m[1],width:p,height:this.boundingRect.y+this.boundingRect.height-m[1],fill:this.barData.fill,strokeWidth:0,strokeFill:this.barData.fill}))}]}}class SHe{constructor(a,f,p){this.chartConfig=a,this.chartData=f,this.chartThemeConfig=p,this.boundingRect={x:0,y:0,width:0,height:0}}setAxes(a,f){this.xAxis=a,this.yAxis=f}setBoundingBoxXY(a){this.boundingRect.x=a.x,this.boundingRect.y=a.y}calculateSpace(a){return this.boundingRect.width=a.width,this.boundingRect.height=a.height,{width:this.boundingRect.width,height:this.boundingRect.height}}getDrawableElements(){if(!(this.xAxis&&this.yAxis))throw Error("Axes must be passed to render Plots");const a=[];for(const[f,p]of this.chartData.plots.entries())switch(p.type){case"line":{const w=new CHe(p,this.xAxis,this.yAxis,this.chartConfig.chartOrientation,f);a.push(...w.getDrawableElement())}break;case"bar":{const w=new _He(p,this.boundingRect,this.xAxis,this.yAxis,this.chartConfig.chartOrientation,f);a.push(...w.getDrawableElement())}break}return a}}function AHe(i,a,f){return new SHe(i,a,f)}class LHe{constructor(a,f,p,w){this.chartConfig=a,this.chartData=f,this.componentStore={title:THe(a,f,p,w),plot:AHe(a,f,p),xAxis:dRt(f.xAxis,a.xAxis,{titleColor:p.xAxisTitleColor,labelColor:p.xAxisLabelColor,tickColor:p.xAxisTickColor,axisLineColor:p.xAxisLineColor},w),yAxis:dRt(f.yAxis,a.yAxis,{titleColor:p.yAxisTitleColor,labelColor:p.yAxisLabelColor,tickColor:p.yAxisTickColor,axisLineColor:p.yAxisLineColor},w)}}calculateVerticalSpace(){let a=this.chartConfig.width,f=this.chartConfig.height,p=0,w=0,m=Math.floor(a*this.chartConfig.plotReservedSpacePercent/100),b=Math.floor(f*this.chartConfig.plotReservedSpacePercent/100),E=this.componentStore.plot.calculateSpace({width:m,height:b});a-=E.width,f-=E.height,E=this.componentStore.title.calculateSpace({width:this.chartConfig.width,height:f}),w=E.height,f-=E.height,this.componentStore.xAxis.setAxisPosition("bottom"),E=this.componentStore.xAxis.calculateSpace({width:a,height:f}),f-=E.height,this.componentStore.yAxis.setAxisPosition("left"),E=this.componentStore.yAxis.calculateSpace({width:a,height:f}),p=E.width,a-=E.width,a>0&&(m+=a,a=0),f>0&&(b+=f,f=0),this.componentStore.plot.calculateSpace({width:m,height:b}),this.componentStore.plot.setBoundingBoxXY({x:p,y:w}),this.componentStore.xAxis.setRange([p,p+m]),this.componentStore.xAxis.setBoundingBoxXY({x:p,y:w+b}),this.componentStore.yAxis.setRange([w,w+b]),this.componentStore.yAxis.setBoundingBoxXY({x:0,y:w}),this.chartData.plots.some(_=>oRt(_))&&this.componentStore.xAxis.recalculateOuterPaddingToDrawBar()}calculateHorizonatalSpace(){let a=this.chartConfig.width,f=this.chartConfig.height,p=0,w=0,m=0,b=Math.floor(a*this.chartConfig.plotReservedSpacePercent/100),E=Math.floor(f*this.chartConfig.plotReservedSpacePercent/100),_=this.componentStore.plot.calculateSpace({width:b,height:E});a-=_.width,f-=_.height,_=this.componentStore.title.calculateSpace({width:this.chartConfig.width,height:f}),p=_.height,f-=_.height,this.componentStore.xAxis.setAxisPosition("left"),_=this.componentStore.xAxis.calculateSpace({width:a,height:f}),a-=_.width,w=_.width,this.componentStore.yAxis.setAxisPosition("top"),_=this.componentStore.yAxis.calculateSpace({width:a,height:f}),f-=_.height,m=p+_.height,a>0&&(b+=a,a=0),f>0&&(E+=f,f=0),this.componentStore.plot.calculateSpace({width:b,height:E}),this.componentStore.plot.setBoundingBoxXY({x:w,y:m}),this.componentStore.yAxis.setRange([w,w+b]),this.componentStore.yAxis.setBoundingBoxXY({x:w,y:p}),this.componentStore.xAxis.setRange([m,m+E]),this.componentStore.xAxis.setBoundingBoxXY({x:0,y:m}),this.chartData.plots.some(A=>oRt(A))&&this.componentStore.xAxis.recalculateOuterPaddingToDrawBar()}calculateSpace(){this.chartConfig.chartOrientation==="horizontal"?this.calculateHorizonatalSpace():this.calculateVerticalSpace()}getDrawableElement(){this.calculateSpace();const a=[];this.componentStore.plot.setAxes(this.componentStore.xAxis,this.componentStore.yAxis);for(const f of Object.values(this.componentStore))a.push(...f.getDrawableElements());return a}}class MHe{static build(a,f,p,w){return new LHe(a,f,p,w).getDrawableElement()}}let RF=0,gRt,jF=bRt(),$F=pRt(),fu=wRt(),cgt=$F.plotColorPalette.split(",").map(i=>i.trim()),BY=!1,ugt=!1;function pRt(){const i=X1t(),a=Fd();return rF(i.xyChart,a.themeVariables.xyChart)}function bRt(){const i=Fd();return rF(Zh.xyChart,i.xyChart)}function wRt(){return{yAxis:{type:"linear",title:"",min:1/0,max:-1/0},xAxis:{type:"band",title:"",categories:[]},title:"",plots:[]}}function lgt(i){const a=Fd();return Q1(i.trim(),a)}function DHe(i){gRt=i}function IHe(i){i==="horizontal"?jF.chartOrientation="horizontal":jF.chartOrientation="vertical"}function OHe(i){fu.xAxis.title=lgt(i.text)}function vRt(i,a){fu.xAxis={type:"linear",title:fu.xAxis.title,min:i,max:a},BY=!0}function 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22:this.$={type:"activeStart",signalType:se.LINETYPE.ACTIVE_START,actor:te[de-1]};break;case 23:this.$={type:"activeEnd",signalType:se.LINETYPE.ACTIVE_END,actor:te[de-1]};break;case 29:se.setDiagramTitle(te[de].substring(6)),this.$=te[de].substring(6);break;case 30:se.setDiagramTitle(te[de].substring(7)),this.$=te[de].substring(7);break;case 31:this.$=te[de].trim(),se.setAccTitle(this.$);break;case 32:case 33:this.$=te[de].trim(),se.setAccDescription(this.$);break;case 34:te[de-1].unshift({type:"loopStart",loopText:se.parseMessage(te[de-2]),signalType:se.LINETYPE.LOOP_START}),te[de-1].push({type:"loopEnd",loopText:te[de-2],signalType:se.LINETYPE.LOOP_END}),this.$=te[de-1];break;case 35:te[de-1].unshift({type:"rectStart",color:se.parseMessage(te[de-2]),signalType:se.LINETYPE.RECT_START}),te[de-1].push({type:"rectEnd",color:se.parseMessage(te[de-2]),signalType:se.LINETYPE.RECT_END}),this.$=te[de-1];break;case 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49:te[de-1].draw="participant",te[de-1].type="addParticipant",this.$=te[de-1];break;case 50:te[de-3].draw="actor",te[de-3].type="addParticipant",te[de-3].description=se.parseMessage(te[de-1]),this.$=te[de-3];break;case 51:te[de-1].draw="actor",te[de-1].type="addParticipant",this.$=te[de-1];break;case 52:te[de-1].type="destroyParticipant",this.$=te[de-1];break;case 53:this.$=[te[de-1],{type:"addNote",placement:te[de-2],actor:te[de-1].actor,text:te[de]}];break;case 54:te[de-2]=[].concat(te[de-1],te[de-1]).slice(0,2),te[de-2][0]=te[de-2][0].actor,te[de-2][1]=te[de-2][1].actor,this.$=[te[de-1],{type:"addNote",placement:se.PLACEMENT.OVER,actor:te[de-2].slice(0,2),text:te[de]}];break;case 55:this.$=[te[de-1],{type:"addLinks",actor:te[de-1].actor,text:te[de]}];break;case 56:this.$=[te[de-1],{type:"addALink",actor:te[de-1].actor,text:te[de]}];break;case 57:this.$=[te[de-1],{type:"addProperties",actor:te[de-1].actor,text:te[de]}];break;case 58:this.$=[te[de-1],{type:"addDetails",actor:te[de-1].actor,text:te[de]}];break;case 61:this.$=[te[de-2],te[de]];break;case 62:this.$=te[de];break;case 63:this.$=se.PLACEMENT.LEFTOF;break;case 64:this.$=se.PLACEMENT.RIGHTOF;break;case 65:this.$=[te[de-4],te[de-1],{type:"addMessage",from:te[de-4].actor,to:te[de-1].actor,signalType:te[de-3],msg:te[de],activate:!0},{type:"activeStart",signalType:se.LINETYPE.ACTIVE_START,actor:te[de-1]}];break;case 66:this.$=[te[de-4],te[de-1],{type:"addMessage",from:te[de-4].actor,to:te[de-1].actor,signalType:te[de-3],msg:te[de]},{type:"activeEnd",signalType:se.LINETYPE.ACTIVE_END,actor:te[de-4]}];break;case 67:this.$=[te[de-3],te[de-1],{type:"addMessage",from:te[de-3].actor,to:te[de-1].actor,signalType:te[de-2],msg:te[de]}];break;case 68:this.$={type:"addParticipant",actor:te[de]};break;case 69:this.$=se.LINETYPE.SOLID_OPEN;break;case 70:this.$=se.LINETYPE.DOTTED_OPEN;break;case 71:this.$=se.LINETYPE.SOLID;break;case 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re=new Error(ke);throw re.hash=zt,re}},parse:function(ke){var zt=this,re=[0],se=[],Pe=[null],te=[],Me=this.table,de="",on=0,ni=0,Ks=2,ws=1,fo=te.slice.call(arguments,1),Xi=Object.create(this.lexer),Er={yy:{}};for(var Xn in this.yy)Object.prototype.hasOwnProperty.call(this.yy,Xn)&&(Er.yy[Xn]=this.yy[Xn]);Xi.setInput(ke,Er.yy),Er.yy.lexer=Xi,Er.yy.parser=this,typeof Xi.yylloc>"u"&&(Xi.yylloc={});var di=Xi.yylloc;te.push(di);var Ee=Xi.options&&Xi.options.ranges;typeof Er.yy.parseError=="function"?this.parseError=Er.yy.parseError:this.parseError=Object.getPrototypeOf(this).parseError;function Kn(){var zs;return zs=se.pop()||Xi.lex()||ws,typeof zs!="number"&&(zs instanceof Array&&(se=zs,zs=se.pop()),zs=zt.symbols_[zs]||zs),zs}for(var He,Ti,pn,Es,qa={},Ma,Gs,Po,vs;;){if(Ti=re[re.length-1],this.defaultActions[Ti]?pn=this.defaultActions[Ti]:((He===null||typeof He>"u")&&(He=Kn()),pn=Me[Ti]&&Me[Ti][He]),typeof pn>"u"||!pn.length||!pn[0]){var ru="";vs=[];for(Ma in Me[Ti])this.terminals_[Ma]&&Ma>Ks&&vs.push("'"+this.terminals_[Ma]+"'");Xi.showPosition?ru="Parse error on line "+(on+1)+`: +`+Xi.showPosition()+` +Expecting `+vs.join(", ")+", got '"+(this.terminals_[He]||He)+"'":ru="Parse error on line "+(on+1)+": Unexpected "+(He==ws?"end of input":"'"+(this.terminals_[He]||He)+"'"),this.parseError(ru,{text:Xi.match,token:this.terminals_[He]||He,line:Xi.yylineno,loc:di,expected:vs})}if(pn[0]instanceof Array&&pn.length>1)throw new Error("Parse Error: multiple actions possible at state: "+Ti+", token: "+He);switch(pn[0]){case 1:re.push(He),Pe.push(Xi.yytext),te.push(Xi.yylloc),re.push(pn[1]),He=null,ni=Xi.yyleng,de=Xi.yytext,on=Xi.yylineno,di=Xi.yylloc;break;case 2:if(Gs=this.productions_[pn[1]][1],qa.$=Pe[Pe.length-Gs],qa._$={first_line:te[te.length-(Gs||1)].first_line,last_line:te[te.length-1].last_line,first_column:te[te.length-(Gs||1)].first_column,last_column:te[te.length-1].last_column},Ee&&(qa._$.range=[te[te.length-(Gs||1)].range[0],te[te.length-1].range[1]]),Es=this.performAction.apply(qa,[de,ni,on,Er.yy,pn[1],Pe,te].concat(fo)),typeof Es<"u")return Es;Gs&&(re=re.slice(0,-1*Gs*2),Pe=Pe.slice(0,-1*Gs),te=te.slice(0,-1*Gs)),re.push(this.productions_[pn[1]][0]),Pe.push(qa.$),te.push(qa._$),Po=Me[re[re.length-2]][re[re.length-1]],re.push(Po);break;case 3:return!0}}return!0}},Ve=function(){var ce={EOF:1,parseError:function(zt,re){if(this.yy.parser)this.yy.parser.parseError(zt,re);else throw new Error(zt)},setInput:function(ke,zt){return this.yy=zt||this.yy||{},this._input=ke,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var ke=this._input[0];this.yytext+=ke,this.yyleng++,this.offset++,this.match+=ke,this.matched+=ke;var zt=ke.match(/(?:\r\n?|\n).*/g);return zt?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),ke},unput:function(ke){var zt=ke.length,re=ke.split(/(?:\r\n?|\n)/g);this._input=ke+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-zt),this.offset-=zt;var se=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),re.length-1&&(this.yylineno-=re.length-1);var Pe=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:re?(re.length===se.length?this.yylloc.first_column:0)+se[se.length-re.length].length-re[0].length:this.yylloc.first_column-zt},this.options.ranges&&(this.yylloc.range=[Pe[0],Pe[0]+this.yyleng-zt]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){if(this.options.backtrack_lexer)this._backtrack=!0;else return this.parseError("Lexical error on line "+(this.yylineno+1)+`. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true). +`+this.showPosition(),{text:"",token:null,line:this.yylineno});return this},less:function(ke){this.unput(this.match.slice(ke))},pastInput:function(){var ke=this.matched.substr(0,this.matched.length-this.match.length);return(ke.length>20?"...":"")+ke.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var ke=this.match;return ke.length<20&&(ke+=this._input.substr(0,20-ke.length)),(ke.substr(0,20)+(ke.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var ke=this.pastInput(),zt=new Array(ke.length+1).join("-");return ke+this.upcomingInput()+` +`+zt+"^"},test_match:function(ke,zt){var re,se,Pe;if(this.options.backtrack_lexer&&(Pe={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(Pe.yylloc.range=this.yylloc.range.slice(0))),se=ke[0].match(/(?:\r\n?|\n).*/g),se&&(this.yylineno+=se.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:se?se[se.length-1].length-se[se.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+ke[0].length},this.yytext+=ke[0],this.match+=ke[0],this.matches=ke,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(ke[0].length),this.matched+=ke[0],re=this.performAction.call(this,this.yy,this,zt,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),re)return re;if(this._backtrack){for(var te in Pe)this[te]=Pe[te];return!1}return!1},next:function(){if(this.done)return this.EOF;this._input||(this.done=!0);var ke,zt,re,se;this._more||(this.yytext="",this.match="");for(var Pe=this._currentRules(),te=0;tezt[0].length)){if(zt=re,se=te,this.options.backtrack_lexer){if(ke=this.test_match(re,Pe[te]),ke!==!1)return ke;if(this._backtrack){zt=!1;continue}else return!1}else if(!this.options.flex)break}return zt?(ke=this.test_match(zt,Pe[se]),ke!==!1?ke:!1):this._input===""?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+`. Unrecognized text. +`+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){var zt=this.next();return zt||this.lex()},begin:function(zt){this.conditionStack.push(zt)},popState:function(){var zt=this.conditionStack.length-1;return zt>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(zt){return zt=this.conditionStack.length-1-Math.abs(zt||0),zt>=0?this.conditionStack[zt]:"INITIAL"},pushState:function(zt){this.begin(zt)},stateStackSize:function(){return this.conditionStack.length},options:{"case-insensitive":!0},performAction:function(zt,re,se,Pe){switch(se){case 0:return 5;case 1:break;case 2:break;case 3:break;case 4:break;case 5:break;case 6:return 19;case 7:return this.begin("LINE"),14;case 8:return this.begin("ID"),50;case 9:return this.begin("ID"),52;case 10:return 13;case 11:return this.begin("ID"),53;case 12:return re.yytext=re.yytext.trim(),this.begin("ALIAS"),70;case 13:return this.popState(),this.popState(),this.begin("LINE"),51;case 14:return this.popState(),this.popState(),5;case 15:return this.begin("LINE"),36;case 16:return this.begin("LINE"),37;case 17:return this.begin("LINE"),38;case 18:return this.begin("LINE"),39;case 19:return this.begin("LINE"),49;case 20:return this.begin("LINE"),41;case 21:return this.begin("LINE"),43;case 22:return this.begin("LINE"),48;case 23:return this.begin("LINE"),44;case 24:return this.begin("LINE"),47;case 25:return this.begin("LINE"),46;case 26:return this.popState(),15;case 27:return 16;case 28:return 65;case 29:return 66;case 30:return 59;case 31:return 60;case 32:return 61;case 33:return 62;case 34:return 57;case 35:return 54;case 36:return this.begin("ID"),21;case 37:return this.begin("ID"),23;case 38:return 29;case 39:return 30;case 40:return this.begin("acc_title"),31;case 41:return this.popState(),"acc_title_value";case 42:return this.begin("acc_descr"),33;case 43:return this.popState(),"acc_descr_value";case 44:this.begin("acc_descr_multiline");break;case 45:this.popState();break;case 46:return"acc_descr_multiline_value";case 47:return 6;case 48:return 18;case 49:return 20;case 50:return 64;case 51:return 5;case 52:return re.yytext=re.yytext.trim(),70;case 53:return 73;case 54:return 74;case 55:return 71;case 56:return 72;case 57:return 75;case 58:return 76;case 59:return 77;case 60:return 78;case 61:return 79;case 62:return 68;case 63:return 69;case 64:return 5;case 65:return"INVALID"}},rules:[/^(?:[\n]+)/i,/^(?:\s+)/i,/^(?:((?!\n)\s)+)/i,/^(?:#[^\n]*)/i,/^(?:%(?!\{)[^\n]*)/i,/^(?:[^\}]%%[^\n]*)/i,/^(?:[0-9]+(?=[ \n]+))/i,/^(?:box\b)/i,/^(?:participant\b)/i,/^(?:actor\b)/i,/^(?:create\b)/i,/^(?:destroy\b)/i,/^(?:[^\->:\n,;]+?([\-]*[^\->:\n,;]+?)*?(?=((?!\n)\s)+as(?!\n)\s|[#\n;]|$))/i,/^(?:as\b)/i,/^(?:(?:))/i,/^(?:loop\b)/i,/^(?:rect\b)/i,/^(?:opt\b)/i,/^(?:alt\b)/i,/^(?:else\b)/i,/^(?:par\b)/i,/^(?:par_over\b)/i,/^(?:and\b)/i,/^(?:critical\b)/i,/^(?:option\b)/i,/^(?:break\b)/i,/^(?:(?:[:]?(?:no)?wrap)?[^#\n;]*)/i,/^(?:end\b)/i,/^(?:left of\b)/i,/^(?:right of\b)/i,/^(?:links\b)/i,/^(?:link\b)/i,/^(?:properties\b)/i,/^(?:details\b)/i,/^(?:over\b)/i,/^(?:note\b)/i,/^(?:activate\b)/i,/^(?:deactivate\b)/i,/^(?:title\s[^#\n;]+)/i,/^(?:title:\s[^#\n;]+)/i,/^(?:accTitle\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*\{\s*)/i,/^(?:[\}])/i,/^(?:[^\}]*)/i,/^(?:sequenceDiagram\b)/i,/^(?:autonumber\b)/i,/^(?:off\b)/i,/^(?:,)/i,/^(?:;)/i,/^(?:[^\+\->:\n,;]+((?!(-x|--x|-\)|--\)))[\-]*[^\+\->:\n,;]+)*)/i,/^(?:->>)/i,/^(?:-->>)/i,/^(?:->)/i,/^(?:-->)/i,/^(?:-[x])/i,/^(?:--[x])/i,/^(?:-[\)])/i,/^(?:--[\)])/i,/^(?::(?:(?:no)?wrap)?[^#\n;]+)/i,/^(?:\+)/i,/^(?:-)/i,/^(?:$)/i,/^(?:.)/i],conditions:{acc_descr_multiline:{rules:[45,46],inclusive:!1},acc_descr:{rules:[43],inclusive:!1},acc_title:{rules:[41],inclusive:!1},ID:{rules:[2,3,12],inclusive:!1},ALIAS:{rules:[2,3,13,14],inclusive:!1},LINE:{rules:[2,3,26],inclusive:!1},INITIAL:{rules:[0,1,3,4,5,6,7,8,9,10,11,15,16,17,18,19,20,21,22,23,24,25,27,28,29,30,31,32,33,34,35,36,37,38,39,40,42,44,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65],inclusive:!0}}};return ce}();me.lexer=Ve;function Ye(){this.yy={}}return Ye.prototype=me,me.Parser=Ye,new Ye}();ggt.parser=ggt;const tVe=ggt;let HF,R5={},pgt={},bgt={},dL=[],zb=[],RY=!1,wgt,j5,VF,gL;const eVe=function(i){dL.push({name:i.text,wrap:i.wrap===void 0&&CT()||!!i.wrap,fill:i.color,actorKeys:[]}),j5=dL.slice(-1)[0]},vgt=function(i,a,f,p){let w=j5;const m=R5[i];if(m){if(j5&&m.box&&j5!==m.box)throw new Error("A same participant should only be defined in one Box: "+m.name+" can't be in '"+m.box.name+"' and in '"+j5.name+"' at the same time.");if(w=m.box?m.box:j5,m.box=w,m&&a===m.name&&f==null)return}(f==null||f.text==null)&&(f={text:a,wrap:null,type:p}),(p==null||f.text==null)&&(f={text:a,wrap:null,type:p}),R5[i]={box:w,name:a,description:f.text,wrap:f.wrap===void 0&&CT()||!!f.wrap,prevActor:HF,links:{},properties:{},actorCnt:null,rectData:null,type:p||"participant"},HF&&R5[HF]&&(R5[HF].nextActor=i),j5&&j5.actorKeys.push(i),HF=i},nVe=i=>{let a,f=0;for(a=0;a>-",token:"->>-",line:"1",loc:{first_line:1,last_line:1,first_column:1,last_column:1},expected:["'ACTIVE_PARTICIPANT'"]},b}return zb.push({from:i,to:a,message:f.text,wrap:f.wrap===void 0&&CT()||!!f.wrap,type:p,activate:w}),!0},iVe=function(){return dL.length>0},sVe=function(){return dL.some(i=>i.name)},aVe=function(){return zb},oVe=function(){return dL},cVe=function(){return R5},uVe=function(){return pgt},lVe=function(){return bgt},GF=function(i){return R5[i]},hVe=function(){return Object.keys(R5)},fVe=function(){RY=!0},dVe=function(){RY=!1},gVe=()=>RY,pVe=function(i){wgt=i},CT=()=>wgt!==void 0?wgt:Oe().sequence.wrap,bVe=function(){R5={},pgt={},bgt={},dL=[],zb=[],RY=!1,hg()},wVe=function(i){const a=i.trim(),f={text:a.replace(/^:?(?:no)?wrap:/,"").trim(),wrap:a.match(/^:?wrap:/)!==null?!0:a.match(/^:?nowrap:/)!==null?!1:void 0};return Ut.debug("parseMessage:",f),f},vVe=function(i){const a=i.match(/^((?:rgba?|hsla?)\s*\(.*\)|\w*)(.*)$/);let f=a!=null&&a[1]?a[1].trim():"transparent",p=a!=null&&a[2]?a[2].trim():void 0;if(window&&window.CSS)window.CSS.supports("color",f)||(f="transparent",p=i.trim());else{const m=new Option().style;m.color=f,m.color!==f&&(f="transparent",p=i.trim())}return{color:f,text:p!==void 0?Q1(p.replace(/^:?(?:no)?wrap:/,""),Oe()):void 0,wrap:p!==void 0?p.match(/^:?wrap:/)!==null?!0:p.match(/^:?nowrap:/)!==null?!1:void 0:void 0}},UF={SOLID:0,DOTTED:1,NOTE:2,SOLID_CROSS:3,DOTTED_CROSS:4,SOLID_OPEN:5,DOTTED_OPEN:6,LOOP_START:10,LOOP_END:11,ALT_START:12,ALT_ELSE:13,ALT_END:14,OPT_START:15,OPT_END:16,ACTIVE_START:17,ACTIVE_END:18,PAR_START:19,PAR_AND:20,PAR_END:21,RECT_START:22,RECT_END:23,SOLID_POINT:24,DOTTED_POINT:25,AUTONUMBER:26,CRITICAL_START:27,CRITICAL_OPTION:28,CRITICAL_END:29,BREAK_START:30,BREAK_END:31,PAR_OVER_START:32},mVe={FILLED:0,OPEN:1},yVe={LEFTOF:0,RIGHTOF:1,OVER:2},_Rt=function(i,a,f){f.text,f.wrap===void 0&&CT()||f.wrap;const p=[].concat(i,i);zb.push({from:p[0],to:p[1],message:f.text,wrap:f.wrap===void 0&&CT()||!!f.wrap,type:UF.NOTE,placement:a})},SRt=function(i,a){const f=GF(i);try{let p=Q1(a.text,Oe());p=p.replace(/&/g,"&"),p=p.replace(/=/g,"=");const w=JSON.parse(p);mgt(f,w)}catch(p){Ut.error("error while parsing actor link text",p)}},xVe=function(i,a){const f=GF(i);try{const b={};let E=Q1(a.text,Oe());var p=E.indexOf("@");E=E.replace(/&/g,"&"),E=E.replace(/=/g,"=");var w=E.slice(0,p-1).trim(),m=E.slice(p+1).trim();b[w]=m,mgt(f,b)}catch(b){Ut.error("error while parsing actor link text",b)}};function mgt(i,a){if(i.links==null)i.links=a;else for(let f in a)i.links[f]=a[f]}const ARt=function(i,a){const f=GF(i);try{let p=Q1(a.text,Oe());const w=JSON.parse(p);LRt(f,w)}catch(p){Ut.error("error while parsing actor properties text",p)}};function LRt(i,a){if(i.properties==null)i.properties=a;else for(let f in a)i.properties[f]=a[f]}function kVe(){j5=void 0}const MRt=function(i,a){const f=GF(i),p=document.getElementById(a.text);try{const w=p.innerHTML,m=JSON.parse(w);m.properties&&LRt(f,m.properties),m.links&&mgt(f,m.links)}catch(w){Ut.error("error while parsing actor details text",w)}},EVe=function(i,a){if(i!==void 0&&i.properties!==void 0)return i.properties[a]},DRt=function(i){if(Array.isArray(i))i.forEach(function(a){DRt(a)});else switch(i.type){case"sequenceIndex":zb.push({from:void 0,to:void 0,message:{start:i.sequenceIndex,step:i.sequenceIndexStep,visible:i.sequenceVisible},wrap:!1,type:i.signalType});break;case"addParticipant":vgt(i.actor,i.actor,i.description,i.draw);break;case"createParticipant":if(R5[i.actor])throw new Error("It is not possible to have actors with the same id, even if one is destroyed before the next is created. Use 'AS' aliases to simulate the behavior");VF=i.actor,vgt(i.actor,i.actor,i.description,i.draw),pgt[i.actor]=zb.length;break;case"destroyParticipant":gL=i.actor,bgt[i.actor]=zb.length;break;case"activeStart":ef(i.actor,void 0,void 0,i.signalType);break;case"activeEnd":ef(i.actor,void 0,void 0,i.signalType);break;case"addNote":_Rt(i.actor,i.placement,i.text);break;case"addLinks":SRt(i.actor,i.text);break;case"addALink":xVe(i.actor,i.text);break;case"addProperties":ARt(i.actor,i.text);break;case"addDetails":MRt(i.actor,i.text);break;case"addMessage":if(VF){if(i.to!==VF)throw new Error("The created participant "+VF+" does not have an associated creating message after its declaration. Please check the sequence diagram.");VF=void 0}else if(gL){if(i.to!==gL&&i.from!==gL)throw new Error("The destroyed participant "+gL+" does not have an associated destroying message after its declaration. Please check the sequence diagram.");gL=void 0}ef(i.from,i.to,i.msg,i.signalType,i.activate);break;case"boxStart":eVe(i.boxData);break;case"boxEnd":kVe();break;case"loopStart":ef(void 0,void 0,i.loopText,i.signalType);break;case"loopEnd":ef(void 0,void 0,void 0,i.signalType);break;case"rectStart":ef(void 0,void 0,i.color,i.signalType);break;case"rectEnd":ef(void 0,void 0,void 0,i.signalType);break;case"optStart":ef(void 0,void 0,i.optText,i.signalType);break;case"optEnd":ef(void 0,void 0,void 0,i.signalType);break;case"altStart":ef(void 0,void 0,i.altText,i.signalType);break;case"else":ef(void 0,void 0,i.altText,i.signalType);break;case"altEnd":ef(void 0,void 0,void 0,i.signalType);break;case"setAccTitle":E0(i.text);break;case"parStart":ef(void 0,void 0,i.parText,i.signalType);break;case"and":ef(void 0,void 0,i.parText,i.signalType);break;case"parEnd":ef(void 0,void 0,void 0,i.signalType);break;case"criticalStart":ef(void 0,void 0,i.criticalText,i.signalType);break;case"option":ef(void 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} + + .actor-line { + stroke: ${i.actorLineColor}; + } + + .messageLine0 { + stroke-width: 1.5; + stroke-dasharray: none; + stroke: ${i.signalColor}; + } + + .messageLine1 { + stroke-width: 1.5; + stroke-dasharray: 2, 2; + stroke: ${i.signalColor}; + } + + #arrowhead path { + fill: ${i.signalColor}; + stroke: ${i.signalColor}; + } + + .sequenceNumber { + fill: ${i.sequenceNumberColor}; + } + + #sequencenumber { + fill: ${i.signalColor}; + } + + #crosshead path { + fill: ${i.signalColor}; + stroke: ${i.signalColor}; + } + + .messageText { + fill: ${i.signalTextColor}; + stroke: none; + } + + .labelBox { + stroke: ${i.labelBoxBorderColor}; + fill: ${i.labelBoxBkgColor}; + } + + .labelText, .labelText > tspan { + fill: ${i.labelTextColor}; + stroke: none; + } + + .loopText, .loopText > tspan { + fill: ${i.loopTextColor}; + stroke: none; + } + + .loopLine { + stroke-width: 2px; + stroke-dasharray: 2, 2; + stroke: ${i.labelBoxBorderColor}; + fill: ${i.labelBoxBorderColor}; + } + + .note { + 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I=w.sequenceItems.length-m+1;w.updateVal(A,"starty",a-I*fn.boxMargin,Math.min),w.updateVal(A,"stopy",p+I*fn.boxMargin,Math.max),w.updateVal(Fr.data,"startx",i-I*fn.boxMargin,Math.min),w.updateVal(Fr.data,"stopx",f+I*fn.boxMargin,Math.max),E!=="activation"&&(w.updateVal(A,"startx",i-I*fn.boxMargin,Math.min),w.updateVal(A,"stopx",f+I*fn.boxMargin,Math.max),w.updateVal(Fr.data,"starty",a-I*fn.boxMargin,Math.min),w.updateVal(Fr.data,"stopy",p+I*fn.boxMargin,Math.max))}}this.sequenceItems.forEach(b()),this.activations.forEach(b("activation"))},insert:function(i,a,f,p){const w=Kr.getMin(i,f),m=Kr.getMax(i,f),b=Kr.getMin(a,p),E=Kr.getMax(a,p);this.updateVal(Fr.data,"startx",w,Math.min),this.updateVal(Fr.data,"starty",b,Math.min),this.updateVal(Fr.data,"stopx",m,Math.max),this.updateVal(Fr.data,"stopy",E,Math.max),this.updateBounds(w,b,m,E)},newActivation:function(i,a,f){const p=f[i.from.actor],w=jY(i.from.actor).length||0,m=p.x+p.width/2+(w-1)*fn.activationWidth/2;this.activations.push({startx:m,starty:this.verticalPos+2,stopx:m+fn.activationWidth,stopy:void 0,actor:i.from.actor,anchored:nf.anchorElement(a)})},endActivation:function(i){const a=this.activations.map(function(f){return f.actor}).lastIndexOf(i.from.actor);return this.activations.splice(a,1)[0]},createLoop:function(i={message:void 0,wrap:!1,width:void 0},a){return{startx:void 0,starty:this.verticalPos,stopx:void 0,stopy:void 0,title:i.message,wrap:i.wrap,width:i.width,height:0,fill:a}},newLoop:function(i={message:void 0,wrap:!1,width:void 0},a){this.sequenceItems.push(this.createLoop(i,a))},endLoop:function(){return this.sequenceItems.pop()},isLoopOverlap:function(){return this.sequenceItems.length?this.sequenceItems[this.sequenceItems.length-1].overlap:!1},addSectionToLoop:function(i){const a=this.sequenceItems.pop();a.sections=a.sections||[],a.sectionTitles=a.sectionTitles||[],a.sections.push({y:Fr.getVerticalPos(),height:0}),a.sectionTitles.push(i),this.sequenceItems.push(a)},saveVerticalPos:function(){this.isLoopOverlap()&&(this.savedVerticalPos=this.verticalPos)},resetVerticalPos:function(){this.isLoopOverlap()&&(this.verticalPos=this.savedVerticalPos)},bumpVerticalPos:function(i){this.verticalPos=this.verticalPos+i,this.data.stopy=Kr.getMax(this.data.stopy,this.verticalPos)},getVerticalPos:function(){return this.verticalPos},getBounds:function(){return{bounds:this.data,models:this.models}}},UVe=function(i,a){Fr.bumpVerticalPos(fn.boxMargin),a.height=fn.boxMargin,a.starty=Fr.getVerticalPos();const f=bT();f.x=a.startx,f.y=a.starty,f.width=a.width||fn.width,f.class="note";const p=i.append("g"),w=nf.drawRect(p,f),m=Rdt();m.x=a.startx,m.y=a.starty,m.width=f.width,m.dy="1em",m.text=a.message,m.class="noteText",m.fontFamily=fn.noteFontFamily,m.fontSize=fn.noteFontSize,m.fontWeight=fn.noteFontWeight,m.anchor=fn.noteAlign,m.textMargin=fn.noteMargin,m.valign="center";const b=pL(p,m),E=Math.round(b.map(_=>(_._groups||_)[0][0].getBBox().height).reduce((_,A)=>_+A));w.attr("height",E+2*fn.noteMargin),a.height+=E+2*fn.noteMargin,Fr.bumpVerticalPos(E+2*fn.noteMargin),a.stopy=a.starty+E+2*fn.noteMargin,a.stopx=a.startx+f.width,Fr.insert(a.startx,a.starty,a.stopx,a.stopy),Fr.models.addNote(a)},ST=i=>({fontFamily:i.messageFontFamily,fontSize:i.messageFontSize,fontWeight:i.messageFontWeight}),bL=i=>({fontFamily:i.noteFontFamily,fontSize:i.noteFontSize,fontWeight:i.noteFontWeight}),kgt=i=>({fontFamily:i.actorFontFamily,fontSize:i.actorFontSize,fontWeight:i.actorFontWeight});function WVe(i,a){Fr.bumpVerticalPos(10);const{startx:f,stopx:p,message:w}=a,m=Kr.splitBreaks(w).length,b=$a.calculateTextDimensions(w,ST(fn)),E=b.height/m;a.height+=E,Fr.bumpVerticalPos(E);let _,A=b.height-10;const I=b.width;if(f===p){_=Fr.getVerticalPos()+A,fn.rightAngles||(A+=fn.boxMargin,_=Fr.getVerticalPos()+A),A+=30;const B=Kr.getMax(I/2,fn.width/2);Fr.insert(f-B,Fr.getVerticalPos()-10+A,p+B,Fr.getVerticalPos()+30+A)}else A+=fn.boxMargin,_=Fr.getVerticalPos()+A,Fr.insert(f,_-10,p,_);return Fr.bumpVerticalPos(A),a.height+=A,a.stopy=a.starty+a.height,Fr.insert(a.fromBounds,a.starty,a.toBounds,a.stopy),_}const YVe=function(i,a,f,p){const{startx:w,stopx:m,starty:b,message:E,type:_,sequenceIndex:A,sequenceVisible:I}=a,B=$a.calculateTextDimensions(E,ST(fn)),N=Rdt();N.x=w,N.y=b+10,N.width=m-w,N.class="messageText",N.dy="1em",N.text=E,N.fontFamily=fn.messageFontFamily,N.fontSize=fn.messageFontSize,N.fontWeight=fn.messageFontWeight,N.anchor=fn.messageAlign,N.valign="center",N.textMargin=fn.wrapPadding,N.tspan=!1,pL(i,N);const R=B.width;let z;w===m?fn.rightAngles?z=i.append("path").attr("d",`M ${w},${f} H ${w+Kr.getMax(fn.width/2,R/2)} V ${f+25} H ${w}`):z=i.append("path").attr("d","M "+w+","+f+" C "+(w+60)+","+(f-10)+" "+(w+60)+","+(f+30)+" "+w+","+(f+20)):(z=i.append("line"),z.attr("x1",w),z.attr("y1",f),z.attr("x2",m),z.attr("y2",f)),_===p.db.LINETYPE.DOTTED||_===p.db.LINETYPE.DOTTED_CROSS||_===p.db.LINETYPE.DOTTED_POINT||_===p.db.LINETYPE.DOTTED_OPEN?(z.style("stroke-dasharray","3, 3"),z.attr("class","messageLine1")):z.attr("class","messageLine0");let W="";fn.arrowMarkerAbsolute&&(W=window.location.protocol+"//"+window.location.host+window.location.pathname+window.location.search,W=W.replace(/\(/g,"\\("),W=W.replace(/\)/g,"\\)")),z.attr("stroke-width",2),z.attr("stroke","none"),z.style("fill","none"),(_===p.db.LINETYPE.SOLID||_===p.db.LINETYPE.DOTTED)&&z.attr("marker-end","url("+W+"#arrowhead)"),(_===p.db.LINETYPE.SOLID_POINT||_===p.db.LINETYPE.DOTTED_POINT)&&z.attr("marker-end","url("+W+"#filled-head)"),(_===p.db.LINETYPE.SOLID_CROSS||_===p.db.LINETYPE.DOTTED_CROSS)&&z.attr("marker-end","url("+W+"#crosshead)"),(I||fn.showSequenceNumbers)&&(z.attr("marker-start","url("+W+"#sequencenumber)"),i.append("text").attr("x",w).attr("y",f+4).attr("font-family","sans-serif").attr("font-size","12px").attr("text-anchor","middle").attr("class","sequenceNumber").text(A))},KVe=function(i,a,f,p,w,m,b){let E=0,_=0,A,I=0;for(const B of p){const N=a[B],R=N.box;A&&A!=R&&(b||Fr.models.addBox(A),_+=fn.boxMargin+A.margin),R&&R!=A&&(b||(R.x=E+_,R.y=w),_+=R.margin),N.width=N.width||fn.width,N.height=Kr.getMax(N.height||fn.height,fn.height),N.margin=N.margin||fn.actorMargin,I=Kr.getMax(I,N.height),f[N.name]&&(_+=N.width/2),N.x=E+_,N.starty=Fr.getVerticalPos(),Fr.insert(N.x,w,N.x+N.width,N.height),E+=N.width+_,N.box&&(N.box.width=E+R.margin-N.box.x),_=N.margin,A=N.box,Fr.models.addActor(N)}A&&!b&&Fr.models.addBox(A),Fr.bumpVerticalPos(I)},Egt=function(i,a,f,p){if(p){let w=0;Fr.bumpVerticalPos(fn.boxMargin*2);for(const m of f){const b=a[m];b.stopy||(b.stopy=Fr.getVerticalPos());const E=nf.drawActor(i,b,fn,!0);w=Kr.getMax(w,E)}Fr.bumpVerticalPos(w+fn.boxMargin)}else for(const w of f){const m=a[w];nf.drawActor(i,m,fn,!1)}},RRt=function(i,a,f,p){let w=0,m=0;for(const b of f){const E=a[b],_=JVe(E),A=nf.drawPopup(i,E,_,fn,fn.forceMenus,p);A.height>w&&(w=A.height),A.width+E.x>m&&(m=A.width+E.x)}return{maxHeight:w,maxWidth:m}},jRt=function(i){Z1(fn,i),i.fontFamily&&(fn.actorFontFamily=fn.noteFontFamily=fn.messageFontFamily=i.fontFamily),i.fontSize&&(fn.actorFontSize=fn.noteFontSize=fn.messageFontSize=i.fontSize),i.fontWeight&&(fn.actorFontWeight=fn.noteFontWeight=fn.messageFontWeight=i.fontWeight)},jY=function(i){return Fr.activations.filter(function(a){return a.actor===i})},$Rt=function(i,a){const f=a[i],p=jY(i),w=p.reduce(function(b,E){return Kr.getMin(b,E.startx)},f.x+f.width/2-1),m=p.reduce(function(b,E){return Kr.getMax(b,E.stopx)},f.x+f.width/2+1);return[w,m]};function k3(i,a,f,p,w){Fr.bumpVerticalPos(f);let m=p;if(a.id&&a.message&&i[a.id]){const b=i[a.id].width,E=ST(fn);a.message=$a.wrapLabel(`[${a.message}]`,b-2*fn.wrapPadding,E),a.width=b,a.wrap=!0;const _=$a.calculateTextDimensions(a.message,E),A=Kr.getMax(_.height,fn.labelBoxHeight);m=p+A,Ut.debug(`${A} - ${a.message}`)}w(a),Fr.bumpVerticalPos(m)}function XVe(i,a,f,p,w,m,b){function E(A,I){A.x{Et.add(Z.from),Et.add(Z.to)}),z=z.filter(Z=>Et.has(Z))}KVe(A,I,B,z,0,W,!1);const mt=rGe(W,I,bt,p);nf.insertArrowHead(A),nf.insertArrowCrossHead(A),nf.insertArrowFilledHead(A),nf.insertSequenceNumber(A);function yt(Et,Z){const Ct=Fr.endActivation(Et);Ct.starty+18>Z&&(Ct.starty=Z-6,Z+=12),nf.drawActivation(A,Ct,Z,fn,jY(Et.from.actor).length),Fr.insert(Ct.startx,Z-10,Ct.stopx,Z)}let ft=1,ut=1;const vt=[],X=[];W.forEach(function(Et,Z){let Ct,xt,Ht;switch(Et.type){case p.db.LINETYPE.NOTE:Fr.resetVerticalPos(),xt=Et.noteModel,UVe(A,xt);break;case p.db.LINETYPE.ACTIVE_START:Fr.newActivation(Et,A,I);break;case p.db.LINETYPE.ACTIVE_END:yt(Et,Fr.getVerticalPos());break;case p.db.LINETYPE.LOOP_START:k3(mt,Et,fn.boxMargin,fn.boxMargin+fn.boxTextMargin,Le=>Fr.newLoop(Le));break;case p.db.LINETYPE.LOOP_END:Ct=Fr.endLoop(),nf.drawLoop(A,Ct,"loop",fn),Fr.bumpVerticalPos(Ct.stopy-Fr.getVerticalPos()),Fr.models.addLoop(Ct);break;case p.db.LINETYPE.RECT_START:k3(mt,Et,fn.boxMargin,fn.boxMargin,Le=>Fr.newLoop(void 0,Le.message));break;case p.db.LINETYPE.RECT_END:Ct=Fr.endLoop(),X.push(Ct),Fr.models.addLoop(Ct),Fr.bumpVerticalPos(Ct.stopy-Fr.getVerticalPos());break;case p.db.LINETYPE.OPT_START:k3(mt,Et,fn.boxMargin,fn.boxMargin+fn.boxTextMargin,Le=>Fr.newLoop(Le));break;case p.db.LINETYPE.OPT_END:Ct=Fr.endLoop(),nf.drawLoop(A,Ct,"opt",fn),Fr.bumpVerticalPos(Ct.stopy-Fr.getVerticalPos()),Fr.models.addLoop(Ct);break;case p.db.LINETYPE.ALT_START:k3(mt,Et,fn.boxMargin,fn.boxMargin+fn.boxTextMargin,Le=>Fr.newLoop(Le));break;case p.db.LINETYPE.ALT_ELSE:k3(mt,Et,fn.boxMargin+fn.boxTextMargin,fn.boxMargin,Le=>Fr.addSectionToLoop(Le));break;case p.db.LINETYPE.ALT_END:Ct=Fr.endLoop(),nf.drawLoop(A,Ct,"alt",fn),Fr.bumpVerticalPos(Ct.stopy-Fr.getVerticalPos()),Fr.models.addLoop(Ct);break;case p.db.LINETYPE.PAR_START:case p.db.LINETYPE.PAR_OVER_START:k3(mt,Et,fn.boxMargin,fn.boxMargin+fn.boxTextMargin,Le=>Fr.newLoop(Le)),Fr.saveVerticalPos();break;case p.db.LINETYPE.PAR_AND:k3(mt,Et,fn.boxMargin+fn.boxTextMargin,fn.boxMargin,Le=>Fr.addSectionToLoop(Le));break;case p.db.LINETYPE.PAR_END:Ct=Fr.endLoop(),nf.drawLoop(A,Ct,"par",fn),Fr.bumpVerticalPos(Ct.stopy-Fr.getVerticalPos()),Fr.models.addLoop(Ct);break;case p.db.LINETYPE.AUTONUMBER:ft=Et.message.start||ft,ut=Et.message.step||ut,Et.message.visible?p.db.enableSequenceNumbers():p.db.disableSequenceNumbers();break;case p.db.LINETYPE.CRITICAL_START:k3(mt,Et,fn.boxMargin,fn.boxMargin+fn.boxTextMargin,Le=>Fr.newLoop(Le));break;case p.db.LINETYPE.CRITICAL_OPTION:k3(mt,Et,fn.boxMargin+fn.boxTextMargin,fn.boxMargin,Le=>Fr.addSectionToLoop(Le));break;case p.db.LINETYPE.CRITICAL_END:Ct=Fr.endLoop(),nf.drawLoop(A,Ct,"critical",fn),Fr.bumpVerticalPos(Ct.stopy-Fr.getVerticalPos()),Fr.models.addLoop(Ct);break;case p.db.LINETYPE.BREAK_START:k3(mt,Et,fn.boxMargin,fn.boxMargin+fn.boxTextMargin,Le=>Fr.newLoop(Le));break;case p.db.LINETYPE.BREAK_END:Ct=Fr.endLoop(),nf.drawLoop(A,Ct,"break",fn),Fr.bumpVerticalPos(Ct.stopy-Fr.getVerticalPos()),Fr.models.addLoop(Ct);break;default:try{Ht=Et.msgModel,Ht.starty=Fr.getVerticalPos(),Ht.sequenceIndex=ft,Ht.sequenceVisible=p.db.showSequenceNumbers();const Le=WVe(A,Ht);XVe(Et,Ht,Le,Z,I,B,N),vt.push({messageModel:Ht,lineStartY:Le}),Fr.models.addMessage(Ht)}catch(Le){Ut.error("error while drawing message",Le)}}[p.db.LINETYPE.SOLID_OPEN,p.db.LINETYPE.DOTTED_OPEN,p.db.LINETYPE.SOLID,p.db.LINETYPE.DOTTED,p.db.LINETYPE.SOLID_CROSS,p.db.LINETYPE.DOTTED_CROSS,p.db.LINETYPE.SOLID_POINT,p.db.LINETYPE.DOTTED_POINT].includes(Et.type)&&(ft=ft+ut)}),Ut.debug("createdActors",B),Ut.debug("destroyedActors",N),Egt(A,I,z,!1),vt.forEach(Et=>YVe(A,Et.messageModel,Et.lineStartY,p)),fn.mirrorActors&&Egt(A,I,z,!0),X.forEach(Et=>nf.drawBackgroundRect(A,Et)),FRt(A,I,z,fn),Fr.models.boxes.forEach(function(Et){Et.height=Fr.getVerticalPos()-Et.y,Fr.insert(Et.x,Et.y,Et.x+Et.width,Et.height),Et.startx=Et.x,Et.starty=Et.y,Et.stopx=Et.startx+Et.width,Et.stopy=Et.starty+Et.height,Et.stroke="rgb(0,0,0, 0.5)",nf.drawBox(A,Et,fn)}),st&&Fr.bumpVerticalPos(fn.boxMargin);const pt=RRt(A,I,z,_),{bounds:U}=Fr.getBounds();let Tt=U.stopy-U.starty;Tt{const b=i[m];b.wrap&&(b.description=$a.wrapLabel(b.description,fn.width-2*fn.wrapPadding,kgt(fn)));const E=$a.calculateTextDimensions(b.description,kgt(fn));b.width=b.wrap?fn.width:Kr.getMax(fn.width,E.width+2*fn.wrapPadding),b.height=b.wrap?Kr.getMax(E.height,fn.height):fn.height,p=Kr.getMax(p,b.height)});for(const m in a){const b=i[m];if(!b)continue;const E=i[b.nextActor];if(!E){const B=a[m]+fn.actorMargin-b.width/2;b.margin=Kr.getMax(B,fn.actorMargin);continue}const A=a[m]+fn.actorMargin-b.width/2-E.width/2;b.margin=Kr.getMax(A,fn.actorMargin)}let w=0;return f.forEach(m=>{const b=ST(fn);let E=m.actorKeys.reduce((I,B)=>I+=i[B].width+(i[B].margin||0),0);E-=2*fn.boxTextMargin,m.wrap&&(m.name=$a.wrapLabel(m.name,E-2*fn.wrapPadding,b));const _=$a.calculateTextDimensions(m.name,b);w=Kr.getMax(_.height,w);const A=Kr.getMax(E,_.width+2*fn.wrapPadding);if(m.margin=fn.boxTextMargin,Em.textMaxHeight=w),Kr.getMax(p,fn.height)}const eGe=function(i,a,f){const p=a[i.from].x,w=a[i.to].x,m=i.wrap&&i.message;let b=$a.calculateTextDimensions(m?$a.wrapLabel(i.message,fn.width,bL(fn)):i.message,bL(fn));const E={width:m?fn.width:Kr.getMax(fn.width,b.width+2*fn.noteMargin),height:0,startx:a[i.from].x,stopx:0,starty:0,stopy:0,message:i.message};return i.placement===f.db.PLACEMENT.RIGHTOF?(E.width=m?Kr.getMax(fn.width,b.width):Kr.getMax(a[i.from].width/2+a[i.to].width/2,b.width+2*fn.noteMargin),E.startx=p+(a[i.from].width+fn.actorMargin)/2):i.placement===f.db.PLACEMENT.LEFTOF?(E.width=m?Kr.getMax(fn.width,b.width+2*fn.noteMargin):Kr.getMax(a[i.from].width/2+a[i.to].width/2,b.width+2*fn.noteMargin),E.startx=p-E.width+(a[i.from].width-fn.actorMargin)/2):i.to===i.from?(b=$a.calculateTextDimensions(m?$a.wrapLabel(i.message,Kr.getMax(fn.width,a[i.from].width),bL(fn)):i.message,bL(fn)),E.width=m?Kr.getMax(fn.width,a[i.from].width):Kr.getMax(a[i.from].width,fn.width,b.width+2*fn.noteMargin),E.startx=p+(a[i.from].width-E.width)/2):(E.width=Math.abs(p+a[i.from].width/2-(w+a[i.to].width/2))+fn.actorMargin,E.startx=p2,B=W=>E?-W:W;i.from===i.to?A=_:(i.activate&&!I&&(A+=B(fn.activationWidth/2-1)),[f.db.LINETYPE.SOLID_OPEN,f.db.LINETYPE.DOTTED_OPEN].includes(i.type)||(A+=B(3)));const N=[p,w,m,b],R=Math.abs(_-A);i.wrap&&i.message&&(i.message=$a.wrapLabel(i.message,Kr.getMax(R+2*fn.wrapPadding,fn.width),ST(fn)));const z=$a.calculateTextDimensions(i.message,ST(fn));return{width:Kr.getMax(i.wrap?0:z.width+2*fn.wrapPadding,R+2*fn.wrapPadding,fn.width),height:0,startx:_,stopx:A,starty:0,stopy:0,message:i.message,type:i.type,wrap:i.wrap,fromBounds:Math.min.apply(null,N),toBounds:Math.max.apply(null,N)}},rGe=function(i,a,f,p){const w={},m=[];let b,E,_;return i.forEach(function(A){switch(A.id=$a.random({length:10}),A.type){case p.db.LINETYPE.LOOP_START:case p.db.LINETYPE.ALT_START:case p.db.LINETYPE.OPT_START:case p.db.LINETYPE.PAR_START:case p.db.LINETYPE.PAR_OVER_START:case p.db.LINETYPE.CRITICAL_START:case p.db.LINETYPE.BREAK_START:m.push({id:A.id,msg:A.message,from:Number.MAX_SAFE_INTEGER,to:Number.MIN_SAFE_INTEGER,width:0});break;case p.db.LINETYPE.ALT_ELSE:case p.db.LINETYPE.PAR_AND:case p.db.LINETYPE.CRITICAL_OPTION:A.message&&(b=m.pop(),w[b.id]=b,w[A.id]=b,m.push(b));break;case p.db.LINETYPE.LOOP_END:case p.db.LINETYPE.ALT_END:case p.db.LINETYPE.OPT_END:case p.db.LINETYPE.PAR_END:case p.db.LINETYPE.CRITICAL_END:case p.db.LINETYPE.BREAK_END:b=m.pop(),w[b.id]=b;break;case p.db.LINETYPE.ACTIVE_START:{const B=a[A.from?A.from.actor:A.to.actor],N=jY(A.from?A.from.actor:A.to.actor).length,R=B.x+B.width/2+(N-1)*fn.activationWidth/2,z={startx:R,stopx:R+fn.activationWidth,actor:A.from.actor,enabled:!0};Fr.activations.push(z)}break;case p.db.LINETYPE.ACTIVE_END:{const B=Fr.activations.map(N=>N.actor).lastIndexOf(A.from.actor);delete Fr.activations.splice(B,1)[0]}break}A.placement!==void 0?(E=eGe(A,a,p),A.noteModel=E,m.forEach(B=>{b=B,b.from=Kr.getMin(b.from,E.startx),b.to=Kr.getMax(b.to,E.startx+E.width),b.width=Kr.getMax(b.width,Math.abs(b.from-b.to))-fn.labelBoxWidth})):(_=nGe(A,a,p),A.msgModel=_,_.startx&&_.stopx&&m.length>0&&m.forEach(B=>{if(b=B,_.startx===_.stopx){const 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de[pn])this.terminals_[Gs]&&Gs>ws&&ru.push("'"+this.terminals_[Gs]+"'");Er.showPosition?zs="Parse error on line "+(ni+1)+`: +`+Er.showPosition()+` +Expecting `+ru.join(", ")+", got '"+(this.terminals_[Ti]||Ti)+"'":zs="Parse error on line "+(ni+1)+": Unexpected "+(Ti==fo?"end of input":"'"+(this.terminals_[Ti]||Ti)+"'"),this.parseError(zs,{text:Er.match,token:this.terminals_[Ti]||Ti,line:Er.yylineno,loc:Ee,expected:ru})}if(Es[0]instanceof Array&&Es.length>1)throw new Error("Parse Error: multiple actions possible at state: "+pn+", token: "+Ti);switch(Es[0]){case 1:se.push(Ti),te.push(Er.yytext),Me.push(Er.yylloc),se.push(Es[1]),Ti=null,Ks=Er.yyleng,on=Er.yytext,ni=Er.yylineno,Ee=Er.yylloc;break;case 2:if(Po=this.productions_[Es[1]][1],Ma.$=te[te.length-Po],Ma._$={first_line:Me[Me.length-(Po||1)].first_line,last_line:Me[Me.length-1].last_line,first_column:Me[Me.length-(Po||1)].first_column,last_column:Me[Me.length-1].last_column},Kn&&(Ma._$.range=[Me[Me.length-(Po||1)].range[0],Me[Me.length-1].range[1]]),qa=this.performAction.apply(Ma,[on,Ks,ni,Xn.yy,Es[1],te,Me].concat(Xi)),typeof qa<"u")return qa;Po&&(se=se.slice(0,-1*Po*2),te=te.slice(0,-1*Po),Me=Me.slice(0,-1*Po)),se.push(this.productions_[Es[1]][0]),te.push(Ma.$),Me.push(Ma._$),vs=de[se[se.length-2]][se[se.length-1]],se.push(vs);break;case 3:return!0}}return!0}},Ye=function(){var ke={EOF:1,parseError:function(re,se){if(this.yy.parser)this.yy.parser.parseError(re,se);else throw new Error(re)},setInput:function(zt,re){return this.yy=re||this.yy||{},this._input=zt,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var zt=this._input[0];this.yytext+=zt,this.yyleng++,this.offset++,this.match+=zt,this.matched+=zt;var re=zt.match(/(?:\r\n?|\n).*/g);return re?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),zt},unput:function(zt){var re=zt.length,se=zt.split(/(?:\r\n?|\n)/g);this._input=zt+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-re),this.offset-=re;var Pe=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),se.length-1&&(this.yylineno-=se.length-1);var te=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:se?(se.length===Pe.length?this.yylloc.first_column:0)+Pe[Pe.length-se.length].length-se[0].length:this.yylloc.first_column-re},this.options.ranges&&(this.yylloc.range=[te[0],te[0]+this.yyleng-re]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){if(this.options.backtrack_lexer)this._backtrack=!0;else return this.parseError("Lexical error on line "+(this.yylineno+1)+`. You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true). +`+this.showPosition(),{text:"",token:null,line:this.yylineno});return this},less:function(zt){this.unput(this.match.slice(zt))},pastInput:function(){var zt=this.matched.substr(0,this.matched.length-this.match.length);return(zt.length>20?"...":"")+zt.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var zt=this.match;return zt.length<20&&(zt+=this._input.substr(0,20-zt.length)),(zt.substr(0,20)+(zt.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var zt=this.pastInput(),re=new Array(zt.length+1).join("-");return zt+this.upcomingInput()+` +`+re+"^"},test_match:function(zt,re){var se,Pe,te;if(this.options.backtrack_lexer&&(te={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(te.yylloc.range=this.yylloc.range.slice(0))),Pe=zt[0].match(/(?:\r\n?|\n).*/g),Pe&&(this.yylineno+=Pe.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:Pe?Pe[Pe.length-1].length-Pe[Pe.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+zt[0].length},this.yytext+=zt[0],this.match+=zt[0],this.matches=zt,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(zt[0].length),this.matched+=zt[0],se=this.performAction.call(this,this.yy,this,re,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),se)return se;if(this._backtrack){for(var Me in te)this[Me]=te[Me];return!1}return!1},next:function(){if(this.done)return this.EOF;this._input||(this.done=!0);var zt,re,se,Pe;this._more||(this.yytext="",this.match="");for(var te=this._currentRules(),Me=0;Mere[0].length)){if(re=se,Pe=Me,this.options.backtrack_lexer){if(zt=this.test_match(se,te[Me]),zt!==!1)return zt;if(this._backtrack){re=!1;continue}else return!1}else if(!this.options.flex)break}return re?(zt=this.test_match(re,te[Pe]),zt!==!1?zt:!1):this._input===""?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+`. Unrecognized text. +`+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){var re=this.next();return re||this.lex()},begin:function(re){this.conditionStack.push(re)},popState:function(){var re=this.conditionStack.length-1;return re>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(re){return re=this.conditionStack.length-1-Math.abs(re||0),re>=0?this.conditionStack[re]:"INITIAL"},pushState:function(re){this.begin(re)},stateStackSize:function(){return this.conditionStack.length},options:{},performAction:function(re,se,Pe,te){switch(Pe){case 0:return 52;case 1:return 53;case 2:return 54;case 3:return 55;case 4:break;case 5:break;case 6:return this.begin("acc_title"),30;case 7:return this.popState(),"acc_title_value";case 8:return this.begin("acc_descr"),32;case 9:return this.popState(),"acc_descr_value";case 10:this.begin("acc_descr_multiline");break;case 11:this.popState();break;case 12:return"acc_descr_multiline_value";case 13:return 8;case 14:break;case 15:return 7;case 16:return 7;case 17:return"EDGE_STATE";case 18:this.begin("callback_name");break;case 19:this.popState();break;case 20:this.popState(),this.begin("callback_args");break;case 21:return 69;case 22:this.popState();break;case 23:return 70;case 24:this.popState();break;case 25:return"STR";case 26:this.begin("string");break;case 27:return this.begin("namespace"),39;case 28:return this.popState(),8;case 29:break;case 30:return this.begin("namespace-body"),36;case 31:return this.popState(),38;case 32:return"EOF_IN_STRUCT";case 33:return 8;case 34:break;case 35:return"EDGE_STATE";case 36:return this.begin("class"),43;case 37:return this.popState(),8;case 38:break;case 39:return this.popState(),this.popState(),38;case 40:return this.begin("class-body"),36;case 41:return this.popState(),38;case 42:return"EOF_IN_STRUCT";case 43:return"EDGE_STATE";case 44:return"OPEN_IN_STRUCT";case 45:break;case 46:return"MEMBER";case 47:return 72;case 48:return 65;case 49:return 66;case 50:return 68;case 51:return 49;case 52:return 51;case 53:return 44;case 54:return 45;case 55:return 71;case 56:this.popState();break;case 57:return"GENERICTYPE";case 58:this.begin("generic");break;case 59:this.popState();break;case 60:return"BQUOTE_STR";case 61:this.begin("bqstring");break;case 62:return 67;case 63:return 67;case 64:return 67;case 65:return 67;case 66:return 59;case 67:return 59;case 68:return 61;case 69:return 61;case 70:return 60;case 71:return 58;case 72:return 62;case 73:return 63;case 74:return 64;case 75:return 21;case 76:return 41;case 77:return 84;case 78:return"DOT";case 79:return"PLUS";case 80:return 81;case 81:return"EQUALS";case 82:return"EQUALS";case 83:return 88;case 84:return 12;case 85:return 14;case 86:return"PUNCTUATION";case 87:return 87;case 88:return 86;case 89:return 83;case 90:return 9}},rules:[/^(?:.*direction\s+TB[^\n]*)/,/^(?:.*direction\s+BT[^\n]*)/,/^(?:.*direction\s+RL[^\n]*)/,/^(?:.*direction\s+LR[^\n]*)/,/^(?:%%(?!\{)*[^\n]*(\r?\n?)+)/,/^(?:%%[^\n]*(\r?\n)*)/,/^(?:accTitle\s*:\s*)/,/^(?:(?!\n||)*[^\n]*)/,/^(?:accDescr\s*:\s*)/,/^(?:(?!\n||)*[^\n]*)/,/^(?:accDescr\s*\{\s*)/,/^(?:[\}])/,/^(?:[^\}]*)/,/^(?:\s*(\r?\n)+)/,/^(?:\s+)/,/^(?:classDiagram-v2\b)/,/^(?:classDiagram\b)/,/^(?:\[\*\])/,/^(?:call[\s]+)/,/^(?:\([\s]*\))/,/^(?:\()/,/^(?:[^(]*)/,/^(?:\))/,/^(?:[^)]*)/,/^(?:["])/,/^(?:[^"]*)/,/^(?:["])/,/^(?:namespace\b)/,/^(?:\s*(\r?\n)+)/,/^(?:\s+)/,/^(?:[{])/,/^(?:[}])/,/^(?:$)/,/^(?:\s*(\r?\n)+)/,/^(?:\s+)/,/^(?:\[\*\])/,/^(?:class\b)/,/^(?:\s*(\r?\n)+)/,/^(?:\s+)/,/^(?:[}])/,/^(?:[{])/,/^(?:[}])/,/^(?:$)/,/^(?:\[\*\])/,/^(?:[{])/,/^(?:[\n])/,/^(?:[^{}\n]*)/,/^(?:cssClass\b)/,/^(?:callback\b)/,/^(?:link\b)/,/^(?:click\b)/,/^(?:note 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xk[i]},getNamespaces:function(){return xk}},KRt=i=>`g.classGroup text { + fill: ${i.nodeBorder||i.classText}; + stroke: none; + font-family: ${i.fontFamily}; + font-size: 10px; + + .title { + font-weight: bolder; + } + +} + +.nodeLabel, .edgeLabel { + color: ${i.classText}; +} +.edgeLabel .label rect { + fill: ${i.mainBkg}; +} +.label text { + fill: ${i.classText}; +} +.edgeLabel .label span { + background: ${i.mainBkg}; +} + +.classTitle { + font-weight: bolder; +} +.node rect, + .node circle, + .node ellipse, + .node polygon, + .node path { + fill: ${i.mainBkg}; + stroke: ${i.nodeBorder}; + stroke-width: 1px; + } + + +.divider { + stroke: ${i.nodeBorder}; + stroke-width: 1; +} + +g.clickable { + cursor: pointer; +} + +g.classGroup rect { + fill: ${i.mainBkg}; + stroke: ${i.nodeBorder}; +} + +g.classGroup line { + stroke: ${i.nodeBorder}; + stroke-width: 1; +} + +.classLabel .box { + stroke: none; + stroke-width: 0; + fill: ${i.mainBkg}; + opacity: 0.5; +} + +.classLabel .label { + fill: ${i.nodeBorder}; + font-size: 10px; +} + +.relation { + stroke: ${i.lineColor}; + stroke-width: 1; + fill: none; +} + +.dashed-line{ + stroke-dasharray: 3; +} + +.dotted-line{ + stroke-dasharray: 1 2; +} + +#compositionStart, .composition { + fill: ${i.lineColor} !important; + stroke: ${i.lineColor} !important; + stroke-width: 1; +} + +#compositionEnd, .composition { + fill: ${i.lineColor} !important; + stroke: ${i.lineColor} !important; + stroke-width: 1; +} + +#dependencyStart, .dependency { + fill: ${i.lineColor} !important; + stroke: ${i.lineColor} !important; + stroke-width: 1; +} + +#dependencyStart, .dependency { + fill: ${i.lineColor} !important; + stroke: ${i.lineColor} !important; + stroke-width: 1; +} + +#extensionStart, .extension { + fill: transparent !important; + stroke: ${i.lineColor} !important; + stroke-width: 1; +} + +#extensionEnd, .extension { + fill: transparent !important; + stroke: ${i.lineColor} !important; + stroke-width: 1; +} + +#aggregationStart, .aggregation { + fill: transparent !important; + stroke: ${i.lineColor} !important; + stroke-width: 1; +} + +#aggregationEnd, .aggregation { + fill: transparent !important; + stroke: ${i.lineColor} !important; + stroke-width: 1; +} + +#lollipopStart, .lollipop { + fill: ${i.mainBkg} !important; + stroke: ${i.lineColor} !important; + stroke-width: 1; +} + +#lollipopEnd, .lollipop { + fill: ${i.mainBkg} !important; + stroke: ${i.lineColor} !important; + stroke-width: 1; +} + +.edgeTerminals { + font-size: 11px; +} + +.classTitleText { + text-anchor: middle; + font-size: 18px; + fill: ${i.textColor}; +} +`;let XRt=0;const TGe=function(i,a,f,p,w){const m=function(at){switch(at){case w.db.relationType.AGGREGATION:return"aggregation";case w.db.relationType.EXTENSION:return"extension";case w.db.relationType.COMPOSITION:return"composition";case w.db.relationType.DEPENDENCY:return"dependency";case w.db.relationType.LOLLIPOP:return"lollipop"}};a.points=a.points.filter(at=>!Number.isNaN(at.y));const b=a.points,E=E5().x(function(at){return at.x}).y(function(at){return at.y}).curve(HP),_=i.append("path").attr("d",E(b)).attr("id","edge"+XRt).attr("class","relation");let A="";p.arrowMarkerAbsolute&&(A=window.location.protocol+"//"+window.location.host+window.location.pathname+window.location.search,A=A.replace(/\(/g,"\\("),A=A.replace(/\)/g,"\\)")),f.relation.lineType==1&&_.attr("class","relation dashed-line"),f.relation.lineType==10&&_.attr("class","relation dotted-line"),f.relation.type1!=="none"&&_.attr("marker-start","url("+A+"#"+m(f.relation.type1)+"Start)"),f.relation.type2!=="none"&&_.attr("marker-end","url("+A+"#"+m(f.relation.type2)+"End)");let I,B;const N=a.points.length;let R=$a.calcLabelPosition(a.points);I=R.x,B=R.y;let z,W,et,st;if(N%2!==0&&N>1){let at=$a.calcCardinalityPosition(f.relation.type1!=="none",a.points,a.points[0]),bt=$a.calcCardinalityPosition(f.relation.type2!=="none",a.points,a.points[N-1]);Ut.debug("cardinality_1_point "+JSON.stringify(at)),Ut.debug("cardinality_2_point "+JSON.stringify(bt)),z=at.x,W=at.y,et=bt.x,st=bt.y}if(f.title!==void 0){const at=i.append("g").attr("class","classLabel"),bt=at.append("text").attr("class","label").attr("x",I).attr("y",B).attr("fill","red").attr("text-anchor","middle").text(f.title);window.label=bt;const mt=bt.node().getBBox();at.insert("rect",":first-child").attr("class","box").attr("x",mt.x-p.padding/2).attr("y",mt.y-p.padding/2).attr("width",mt.width+p.padding).attr("height",mt.height+p.padding)}Ut.info("Rendering relation "+JSON.stringify(f)),f.relationTitle1!==void 0&&f.relationTitle1!=="none"&&i.append("g").attr("class","cardinality").append("text").attr("class","type1").attr("x",z).attr("y",W).attr("fill","black").attr("font-size","6").text(f.relationTitle1),f.relationTitle2!==void 0&&f.relationTitle2!=="none"&&i.append("g").attr("class","cardinality").append("text").attr("class","type2").attr("x",et).attr("y",st).attr("fill","black").attr("font-size","6").text(f.relationTitle2),XRt++},CGe=function(i,a,f,p){Ut.debug("Rendering class ",a,f);const w=a.id,m={id:w,label:a.id,width:0,height:0},b=i.append("g").attr("id",p.db.lookUpDomId(w)).attr("class","classGroup");let E;a.link?E=b.append("svg:a").attr("xlink:href",a.link).attr("target",a.linkTarget).append("text").attr("y",f.textHeight+f.padding).attr("x",0):E=b.append("text").attr("y",f.textHeight+f.padding).attr("x",0);let _=!0;a.annotations.forEach(function(bt){const mt=E.append("tspan").text("«"+bt+"»");_||mt.attr("dy",f.textHeight),_=!1});let A=QRt(a);const I=E.append("tspan").text(A).attr("class","title");_||I.attr("dy",f.textHeight);const B=E.node().getBBox().height;let N,R,z;if(a.members.length>0){N=b.append("line").attr("x1",0).attr("y1",f.padding+B+f.dividerMargin/2).attr("y2",f.padding+B+f.dividerMargin/2);const bt=b.append("text").attr("x",f.padding).attr("y",B+f.dividerMargin+f.textHeight).attr("fill","white").attr("class","classText");_=!0,a.members.forEach(function(mt){ZRt(bt,mt,_,f),_=!1}),R=bt.node().getBBox()}if(a.methods.length>0){z=b.append("line").attr("x1",0).attr("y1",f.padding+B+f.dividerMargin+R.height).attr("y2",f.padding+B+f.dividerMargin+R.height);const bt=b.append("text").attr("x",f.padding).attr("y",B+2*f.dividerMargin+R.height+f.textHeight).attr("fill","white").attr("class","classText");_=!0,a.methods.forEach(function(mt){ZRt(bt,mt,_,f),_=!1})}const W=b.node().getBBox();var et=" ";a.cssClasses.length>0&&(et=et+a.cssClasses.join(" "));const at=b.insert("rect",":first-child").attr("x",0).attr("y",0).attr("width",W.width+2*f.padding).attr("height",W.height+f.padding+.5*f.dividerMargin).attr("class",et).node().getBBox().width;return E.node().childNodes.forEach(function(bt){bt.setAttribute("x",(at-bt.getBBox().width)/2)}),a.tooltip&&E.insert("title").text(a.tooltip),N&&N.attr("x2",at),z&&z.attr("x2",at),m.width=at,m.height=W.height+f.padding+.5*f.dividerMargin,m},QRt=function(i){let a=i.id;return i.type&&(a+="<"+YP(i.type)+">"),a},_Ge=function(i,a,f,p){Ut.debug("Rendering note ",a,f);const w=a.id,m={id:w,text:a.text,width:0,height:0},b=i.append("g").attr("id",w).attr("class","classGroup");let E=b.append("text").attr("y",f.textHeight+f.padding).attr("x",0);const _=JSON.parse(`"${a.text}"`).split(` +`);_.forEach(function(N){Ut.debug(`Adding line: ${N}`),E.append("tspan").text(N).attr("class","title").attr("dy",f.textHeight)});const A=b.node().getBBox(),B=b.insert("rect",":first-child").attr("x",0).attr("y",0).attr("width",A.width+2*f.padding).attr("height",A.height+_.length*f.textHeight+f.padding+.5*f.dividerMargin).node().getBBox().width;return E.node().childNodes.forEach(function(N){N.setAttribute("x",(B-N.getBBox().width)/2)}),m.width=B,m.height=A.height+_.length*f.textHeight+f.padding+.5*f.dividerMargin,m},ZRt=function(i,a,f,p){const{displayText:w,cssStyle:m}=a.getDisplayDetails(),b=i.append("tspan").attr("x",p.padding).text(w);m!==""&&b.attr("style",a.cssStyle),f||b.attr("dy",p.textHeight)},Agt={getClassTitleString:QRt,drawClass:CGe,drawEdge:TGe,drawNote:_Ge};let VY={};const GY=20,YF=function(i){const a=Object.entries(VY).find(f=>f[1].label===i);if(a)return a[0]},SGe=function(i){i.append("defs").append("marker").attr("id","extensionStart").attr("class","extension").attr("refX",0).attr("refY",7).attr("markerWidth",190).attr("markerHeight",240).attr("orient","auto").append("path").attr("d","M 1,7 L18,13 V 1 Z"),i.append("defs").append("marker").attr("id","extensionEnd").attr("refX",19).attr("refY",7).attr("markerWidth",20).attr("markerHeight",28).attr("orient","auto").append("path").attr("d","M 1,1 V 13 L18,7 Z"),i.append("defs").append("marker").attr("id","compositionStart").attr("class","extension").attr("refX",0).attr("refY",7).attr("markerWidth",190).attr("markerHeight",240).attr("orient","auto").append("path").attr("d","M 18,7 L9,13 L1,7 L9,1 Z"),i.append("defs").append("marker").attr("id","compositionEnd").attr("refX",19).attr("refY",7).attr("markerWidth",20).attr("markerHeight",28).attr("orient","auto").append("path").attr("d","M 18,7 L9,13 L1,7 L9,1 Z"),i.append("defs").append("marker").attr("id","aggregationStart").attr("class","extension").attr("refX",0).attr("refY",7).attr("markerWidth",190).attr("markerHeight",240).attr("orient","auto").append("path").attr("d","M 18,7 L9,13 L1,7 L9,1 Z"),i.append("defs").append("marker").attr("id","aggregationEnd").attr("refX",19).attr("refY",7).attr("markerWidth",20).attr("markerHeight",28).attr("orient","auto").append("path").attr("d","M 18,7 L9,13 L1,7 L9,1 Z"),i.append("defs").append("marker").attr("id","dependencyStart").attr("class","extension").attr("refX",0).attr("refY",7).attr("markerWidth",190).attr("markerHeight",240).attr("orient","auto").append("path").attr("d","M 5,7 L9,13 L1,7 L9,1 Z"),i.append("defs").append("marker").attr("id","dependencyEnd").attr("refX",19).attr("refY",7).attr("markerWidth",20).attr("markerHeight",28).attr("orient","auto").append("path").attr("d","M 18,7 L9,13 L14,7 L9,1 Z")},AGe=Object.freeze(Object.defineProperty({__proto__:null,diagram:{parser:zRt,db:HY,renderer:{draw:function(i,a,f,p){const w=Oe().class;VY={},Ut.info("Rendering diagram "+i);const m=Oe().securityLevel;let b;m==="sandbox"&&(b=yr("#i"+a));const E=yr(m==="sandbox"?b.nodes()[0].contentDocument.body:"body"),_=E.select(`[id='${a}']`);SGe(_);const A=new c1({multigraph:!0});A.setGraph({isMultiGraph:!0}),A.setDefaultEdgeLabel(function(){return{}});const I=p.db.getClasses(),B=Object.keys(I);for(const at of B){const bt=I[at],mt=Agt.drawClass(_,bt,w,p);VY[mt.id]=mt,A.setNode(mt.id,mt),Ut.info("Org height: "+mt.height)}p.db.getRelations().forEach(function(at){Ut.info("tjoho"+YF(at.id1)+YF(at.id2)+JSON.stringify(at)),A.setEdge(YF(at.id1),YF(at.id2),{relation:at},at.title||"DEFAULT")}),p.db.getNotes().forEach(function(at){Ut.debug(`Adding note: ${JSON.stringify(at)}`);const bt=Agt.drawNote(_,at,w,p);VY[bt.id]=bt,A.setNode(bt.id,bt),at.class&&at.class in I&&A.setEdge(at.id,YF(at.class),{relation:{id1:at.id,id2:at.class,relation:{type1:"none",type2:"none",lineType:10}}},"DEFAULT")}),aL(A),A.nodes().forEach(function(at){at!==void 0&&A.node(at)!==void 0&&(Ut.debug("Node "+at+": 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stroke: black",padding:((A=Oe().flowchart)==null?void 0:A.padding)??((I=Oe().class)==null?void 0:I.padding)};a.setNode(b.id,_),JRt(b.classes,a,f,p,b.id),Ut.info("setNode",_)})},JRt=function(i,a,f,p,w){const m=Object.keys(i);Ut.info("keys:",m),Ut.info(i),m.filter(b=>i[b].parent==w).forEach(function(b){var z,W;const E=i[b],_=E.cssClasses.join(" "),A={labelStyle:"",style:""},I=E.label??E.id,B=0,N="class_box",R={labelStyle:A.labelStyle,shape:N,labelText:Lgt(I),classData:E,rx:B,ry:B,class:_,style:A.style,id:E.id,domId:E.domId,tooltip:p.db.getTooltip(E.id,w)||"",haveCallback:E.haveCallback,link:E.link,width:E.type==="group"?500:void 0,type:E.type,padding:((z=Oe().flowchart)==null?void 0:z.padding)??((W=Oe().class)==null?void 0:W.padding)};a.setNode(E.id,R),w&&a.setParent(E.id,w),Ut.info("setNode",R)})},MGe=function(i,a,f,p){Ut.info(i),i.forEach(function(w,m){var W,et;const b=w,E="",_={labelStyle:"",style:""},A=b.text,I=0,B="note",N={labelStyle:_.labelStyle,shape:B,labelText:Lgt(A),noteData:b,rx:I,ry:I,class:E,style:_.style,id:b.id,domId:b.id,tooltip:"",type:"note",padding:((W=Oe().flowchart)==null?void 0:W.padding)??((et=Oe().class)==null?void 0:et.padding)};if(a.setNode(b.id,N),Ut.info("setNode",N),!b.class||!(b.class in p))return;const R=f+m,z={id:`edgeNote${R}`,classes:"relation",pattern:"dotted",arrowhead:"none",startLabelRight:"",endLabelLeft:"",arrowTypeStart:"none",arrowTypeEnd:"none",style:"fill:none",labelStyle:"",curve:ew(Mgt.curve,cg)};a.setEdge(b.id,b.class,z,R)})},DGe=function(i,a){const f=Oe().flowchart;let p=0;i.forEach(function(w){var b;p++;const m={classes:"relation",pattern:w.relation.lineType==1?"dashed":"solid",id:"id"+p,arrowhead:w.type==="arrow_open"?"none":"normal",startLabelRight:w.relationTitle1==="none"?"":w.relationTitle1,endLabelLeft:w.relationTitle2==="none"?"":w.relationTitle2,arrowTypeStart:tjt(w.relation.type1),arrowTypeEnd:tjt(w.relation.type2),style:"fill:none",labelStyle:"",curve:ew(f==null?void 0:f.curve,cg)};if(Ut.info(m,w),w.style!==void 0){const E=im(w.style);m.style=E.style,m.labelStyle=E.labelStyle}w.text=w.title,w.text===void 0?w.style!==void 0&&(m.arrowheadStyle="fill: #333"):(m.arrowheadStyle="fill: #333",m.labelpos="c",((b=Oe().flowchart)==null?void 0:b.htmlLabels)??Oe().htmlLabels?(m.labelType="html",m.label=''+w.text+""):(m.labelType="text",m.label=w.text.replace(Kr.lineBreakRegex,` +`),w.style===void 0&&(m.style=m.style||"stroke: #333; stroke-width: 1.5px;fill:none"),m.labelStyle=m.labelStyle.replace("color:","fill:"))),a.setEdge(w.id1,w.id2,m,p)})},IGe=function(i){Mgt={...Mgt,...i}},OGe=async 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st=m==="sandbox"?R.nodes()[0].contentDocument:document,at=st.querySelectorAll('[id="'+a+'"] .edgeLabel .label');for(const bt of at){const mt=bt.getBBox(),yt=st.createElementNS("http://www.w3.org/2000/svg","rect");yt.setAttribute("rx",0),yt.setAttribute("ry",0),yt.setAttribute("width",mt.width),yt.setAttribute("height",mt.height),bt.insertBefore(yt,bt.firstChild)}}};function tjt(i){let a;switch(i){case 0:a="aggregation";break;case 1:a="extension";break;case 2:a="composition";break;case 3:a="dependency";break;case 4:a="lollipop";break;default:a="none"}return a}const PGe=Object.freeze(Object.defineProperty({__proto__:null,diagram:{parser:zRt,db:HY,renderer:{setConf:IGe,draw:OGe},styles:KRt,init:i=>{i.class||(i.class={}),i.class.arrowMarkerAbsolute=i.arrowMarkerAbsolute,HY.clear()}}},Symbol.toStringTag,{value:"Module"}));var Dgt=function(){var i=function(Et,Z,Ct,xt){for(Ct=Ct||{},xt=Et.length;xt--;Ct[Et[xt]]=Z);return 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this.popState(),xt.yytext=xt.yytext.slice(0,-8).trim(),25;case 35:return this.popState(),xt.yytext=xt.yytext.slice(0,-10).trim(),26;case 36:return this.popState(),xt.yytext=xt.yytext.slice(0,-8).trim(),24;case 37:return this.popState(),xt.yytext=xt.yytext.slice(0,-8).trim(),25;case 38:return this.popState(),xt.yytext=xt.yytext.slice(0,-10).trim(),26;case 39:return 44;case 40:return 45;case 41:return 46;case 42:return 47;case 43:this.pushState("STATE_STRING");break;case 44:return this.pushState("STATE_ID"),"AS";case 45:return this.popState(),"ID";case 46:this.popState();break;case 47:return"STATE_DESCR";case 48:return 18;case 49:this.popState();break;case 50:return this.popState(),this.pushState("struct"),19;case 51:break;case 52:return this.popState(),20;case 53:break;case 54:return this.begin("NOTE"),28;case 55:return this.popState(),this.pushState("NOTE_ID"),52;case 56:return this.popState(),this.pushState("NOTE_ID"),53;case 57:this.popState(),this.pushState("FLOATING_NOTE");break;case 58:return this.popState(),this.pushState("FLOATING_NOTE_ID"),"AS";case 59:break;case 60:return"NOTE_TEXT";case 61:return this.popState(),"ID";case 62:return this.popState(),this.pushState("NOTE_TEXT"),23;case 63:return this.popState(),xt.yytext=xt.yytext.substr(2).trim(),30;case 64:return this.popState(),xt.yytext=xt.yytext.slice(0,-8).trim(),30;case 65:return 6;case 66:return 6;case 67:return 15;case 68:return 50;case 69:return 23;case 70:return xt.yytext=xt.yytext.trim(),13;case 71:return 14;case 72:return 27;case 73:return 51;case 74:return 5;case 75:return"INVALID"}},rules:[/^(?:default\b)/i,/^(?:.*direction\s+TB[^\n]*)/i,/^(?:.*direction\s+BT[^\n]*)/i,/^(?:.*direction\s+RL[^\n]*)/i,/^(?:.*direction\s+LR[^\n]*)/i,/^(?:%%(?!\{)[^\n]*)/i,/^(?:[^\}]%%[^\n]*)/i,/^(?:[\n]+)/i,/^(?:[\s]+)/i,/^(?:((?!\n)\s)+)/i,/^(?:#[^\n]*)/i,/^(?:%[^\n]*)/i,/^(?:scale\s+)/i,/^(?:\d+)/i,/^(?:\s+width\b)/i,/^(?:accTitle\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*:\s*)/i,/^(?:(?!\n||)*[^\n]*)/i,/^(?:accDescr\s*\{\s*)/i,/^(?:[\}])/i,/^(?:[^\}]*)/i,/^(?:classDef\s+)/i,/^(?:DEFAULT\s+)/i,/^(?:\w+\s+)/i,/^(?:[^\n]*)/i,/^(?:class\s+)/i,/^(?:(\w+)+((,\s*\w+)*))/i,/^(?:[^\n]*)/i,/^(?:scale\s+)/i,/^(?:\d+)/i,/^(?:\s+width\b)/i,/^(?:state\s+)/i,/^(?:.*<>)/i,/^(?:.*<>)/i,/^(?:.*<>)/i,/^(?:.*\[\[fork\]\])/i,/^(?:.*\[\[join\]\])/i,/^(?:.*\[\[choice\]\])/i,/^(?:.*direction\s+TB[^\n]*)/i,/^(?:.*direction\s+BT[^\n]*)/i,/^(?:.*direction\s+RL[^\n]*)/i,/^(?:.*direction\s+LR[^\n]*)/i,/^(?:["])/i,/^(?:\s*as\s+)/i,/^(?:[^\n\{]*)/i,/^(?:["])/i,/^(?:[^"]*)/i,/^(?:[^\n\s\{]+)/i,/^(?:\n)/i,/^(?:\{)/i,/^(?:%%(?!\{)[^\n]*)/i,/^(?:\})/i,/^(?:[\n])/i,/^(?:note\s+)/i,/^(?:left of\b)/i,/^(?:right of\b)/i,/^(?:")/i,/^(?:\s*as\s*)/i,/^(?:["])/i,/^(?:[^"]*)/i,/^(?:[^\n]*)/i,/^(?:\s*[^:\n\s\-]+)/i,/^(?:\s*:[^:\n;]+)/i,/^(?:[\s\S]*?end note\b)/i,/^(?:stateDiagram\s+)/i,/^(?:stateDiagram-v2\s+)/i,/^(?:hide empty description\b)/i,/^(?:\[\*\])/i,/^(?:[^:\n\s\-\{]+)/i,/^(?:\s*:[^:\n;]+)/i,/^(?:-->)/i,/^(?:--)/i,/^(?::::)/i,/^(?:$)/i,/^(?:.)/i],conditions:{LINE:{rules:[9,10],inclusive:!1},struct:{rules:[9,10,22,26,32,39,40,41,42,51,52,53,54,68,69,70,71,72],inclusive:!1},FLOATING_NOTE_ID:{rules:[61],inclusive:!1},FLOATING_NOTE:{rules:[58,59,60],inclusive:!1},NOTE_TEXT:{rules:[63,64],inclusive:!1},NOTE_ID:{rules:[62],inclusive:!1},NOTE:{rules:[55,56,57],inclusive:!1},CLASS_STYLE:{rules:[28],inclusive:!1},CLASS:{rules:[27],inclusive:!1},CLASSDEFID:{rules:[25],inclusive:!1},CLASSDEF:{rules:[23,24],inclusive:!1},acc_descr_multiline:{rules:[20,21],inclusive:!1},acc_descr:{rules:[18],inclusive:!1},acc_title:{rules:[16],inclusive:!1},SCALE:{rules:[13,14,30,31],inclusive:!1},ALIAS:{rules:[],inclusive:!1},STATE_ID:{rules:[45],inclusive:!1},STATE_STRING:{rules:[46,47],inclusive:!1},FORK_STATE:{rules:[],inclusive:!1},STATE:{rules:[9,10,33,34,35,36,37,38,43,44,48,49,50],inclusive:!1},ID:{rules:[9,10],inclusive:!1},INITIAL:{rules:[0,1,2,3,4,5,6,7,8,10,11,12,15,17,19,22,26,29,32,50,54,65,66,67,68,69,70,71,73,74,75],inclusive:!0}}};return Et}();It.lexer=Ot;function Bt(){this.yy={}}return Bt.prototype=It,It.Parser=Bt,new Bt}();Dgt.parser=Dgt;const ejt=Dgt,FGe="LR",NGe="TB",UY="state",Igt="relation",BGe="classDef",RGe="applyClass",KF="default",njt="divider",Ogt="[*]",rjt="start",ijt=Ogt,sjt="end",ajt="color",ojt="fill",jGe="bgFill",$Ge=",";function cjt(){return{}}let ujt=FGe,WY=[],XF=cjt();const ljt=()=>({relations:[],states:{},documents:{}});let YY={root:ljt()},S0=YY.root,QF=0,hjt=0;const zGe={LINE:0,DOTTED_LINE:1},qGe={AGGREGATION:0,EXTENSION:1,COMPOSITION:2,DEPENDENCY:3},KY=i=>JSON.parse(JSON.stringify(i)),HGe=i=>{Ut.info("Setting root doc",i),WY=i},VGe=()=>WY,XY=(i,a,f)=>{if(a.stmt===Igt)XY(i,a.state1,!0),XY(i,a.state2,!1);else if(a.stmt===UY&&(a.id==="[*]"?(a.id=f?i.id+"_start":i.id+"_end",a.start=f):a.id=a.id.trim()),a.doc){const p=[];let w=[],m;for(m=0;m0&&w.length>0){const b={stmt:UY,id:VIt(),type:"divider",doc:KY(w)};p.push(KY(b)),a.doc=p}a.doc.forEach(b=>XY(a,b,!0))}},GGe=()=>(XY({id:"root"},{id:"root",doc:WY},!0),{id:"root",doc:WY}),UGe=i=>{let a;i.doc?a=i.doc:a=i,Ut.info(a),fjt(!0),Ut.info("Extract",a),a.forEach(f=>{switch(f.stmt){case UY:LT(f.id.trim(),f.type,f.doc,f.description,f.note,f.classes,f.styles,f.textStyles);break;case Igt:djt(f.state1,f.state2,f.description);break;case BGe:gjt(f.id.trim(),f.classes);break;case RGe:Bgt(f.id.trim(),f.styleClass);break}})},LT=function(i,a=KF,f=null,p=null,w=null,m=null,b=null,E=null){const _=i==null?void 0:i.trim();S0.states[_]===void 0?(Ut.info("Adding state ",_,p),S0.states[_]={id:_,descriptions:[],type:a,doc:f,note:w,classes:[],styles:[],textStyles:[]}):(S0.states[_].doc||(S0.states[_].doc=f),S0.states[_].type||(S0.states[_].type=a)),p&&(Ut.info("Setting state description",_,p),typeof p=="string"&&Ngt(_,p.trim()),typeof p=="object"&&p.forEach(A=>Ngt(_,A.trim()))),w&&(S0.states[_].note=w,S0.states[_].note.text=Kr.sanitizeText(S0.states[_].note.text,Oe())),m&&(Ut.info("Setting state classes",_,m),(typeof m=="string"?[m]:m).forEach(I=>Bgt(_,I.trim()))),b&&(Ut.info("Setting state styles",_,b),(typeof b=="string"?[b]:b).forEach(I=>nUe(_,I.trim()))),E&&(Ut.info("Setting state styles",_,b),(typeof E=="string"?[E]:E).forEach(I=>rUe(_,I.trim())))},fjt=function(i){YY={root:ljt()},S0=YY.root,QF=0,XF=cjt(),i||hg()},ZF=function(i){return S0.states[i]},WGe=function(){return S0.states},YGe=function(){Ut.info("Documents = ",YY)},KGe=function(){return S0.relations};function Pgt(i=""){let a=i;return i===Ogt&&(QF++,a=`${rjt}${QF}`),a}function Fgt(i="",a=KF){return i===Ogt?rjt:a}function XGe(i=""){let a=i;return i===ijt&&(QF++,a=`${sjt}${QF}`),a}function QGe(i="",a=KF){return i===ijt?sjt:a}function ZGe(i,a,f){let p=Pgt(i.id.trim()),w=Fgt(i.id.trim(),i.type),m=Pgt(a.id.trim()),b=Fgt(a.id.trim(),a.type);LT(p,w,i.doc,i.description,i.note,i.classes,i.styles,i.textStyles),LT(m,b,a.doc,a.description,a.note,a.classes,a.styles,a.textStyles),S0.relations.push({id1:p,id2:m,relationTitle:Kr.sanitizeText(f,Oe())})}const djt=function(i,a,f){if(typeof i=="object")ZGe(i,a,f);else{const p=Pgt(i.trim()),w=Fgt(i),m=XGe(a.trim()),b=QGe(a);LT(p,w),LT(m,b),S0.relations.push({id1:p,id2:m,title:Kr.sanitizeText(f,Oe())})}},Ngt=function(i,a){const f=S0.states[i],p=a.startsWith(":")?a.replace(":","").trim():a;f.descriptions.push(Kr.sanitizeText(p,Oe()))},JGe=function(i){return i.substring(0,1)===":"?i.substr(2).trim():i.trim()},tUe=()=>(hjt++,"divider-id-"+hjt),gjt=function(i,a=""){XF[i]===void 0&&(XF[i]={id:i,styles:[],textStyles:[]});const f=XF[i];a!=null&&a.split($Ge).forEach(p=>{const w=p.replace(/([^;]*);/,"$1").trim();if(p.match(ajt)){const b=w.replace(ojt,jGe).replace(ajt,ojt);f.textStyles.push(b)}f.styles.push(w)})},eUe=function(){return XF},Bgt=function(i,a){i.split(",").forEach(function(f){let p=ZF(f);if(p===void 0){const w=f.trim();LT(w),p=ZF(w)}p.classes.push(a)})},nUe=function(i,a){const f=ZF(i);f!==void 0&&f.textStyles.push(a)},rUe=function(i,a){const f=ZF(i);f!==void 0&&f.textStyles.push(a)},$5={getConfig:()=>Oe().state,addState:LT,clear:fjt,getState:ZF,getStates:WGe,getRelations:KGe,getClasses:eUe,getDirection:()=>ujt,addRelation:djt,getDividerId:tUe,setDirection:i=>{ujt=i},cleanupLabel:JGe,lineType:zGe,relationType:qGe,logDocuments:YGe,getRootDoc:VGe,setRootDoc:HGe,getRootDocV2:GGe,extract:UGe,trimColon:i=>i&&i[0]===":"?i.substr(1).trim():i.trim(),getAccTitle:fg,setAccTitle:E0,getAccDescription:gg,setAccDescription:dg,addStyleClass:gjt,setCssClass:Bgt,addDescription:Ngt,setDiagramTitle:Nb,getDiagramTitle:pg},pjt=i=>` +defs #statediagram-barbEnd { + fill: ${i.transitionColor}; + stroke: ${i.transitionColor}; + } +g.stateGroup text { + fill: ${i.nodeBorder}; + stroke: none; + font-size: 10px; +} +g.stateGroup text { + fill: ${i.textColor}; + stroke: none; + font-size: 10px; + +} +g.stateGroup .state-title { + font-weight: bolder; + fill: ${i.stateLabelColor}; +} + +g.stateGroup rect { + fill: ${i.mainBkg}; + stroke: ${i.nodeBorder}; +} + +g.stateGroup line { + stroke: ${i.lineColor}; + stroke-width: 1; +} + +.transition { + stroke: ${i.transitionColor}; + stroke-width: 1; + fill: none; +} + +.stateGroup .composit { + fill: ${i.background}; + border-bottom: 1px +} + +.stateGroup .alt-composit { + fill: #e0e0e0; + border-bottom: 1px +} + +.state-note { + stroke: ${i.noteBorderColor}; + fill: ${i.noteBkgColor}; + + text { + fill: ${i.noteTextColor}; + stroke: none; + font-size: 10px; + } +} + +.stateLabel .box { + stroke: none; + stroke-width: 0; + fill: ${i.mainBkg}; + opacity: 0.5; +} + +.edgeLabel .label rect { + fill: ${i.labelBackgroundColor}; + opacity: 0.5; +} +.edgeLabel .label text { + fill: ${i.transitionLabelColor||i.tertiaryTextColor}; +} +.label div .edgeLabel { + color: ${i.transitionLabelColor||i.tertiaryTextColor}; +} + +.stateLabel text { + fill: ${i.stateLabelColor}; + font-size: 10px; + font-weight: bold; +} + +.node circle.state-start { + fill: ${i.specialStateColor}; + stroke: ${i.specialStateColor}; +} + +.node .fork-join { + fill: ${i.specialStateColor}; + stroke: ${i.specialStateColor}; +} + +.node circle.state-end { + fill: ${i.innerEndBackground}; + stroke: ${i.background}; + stroke-width: 1.5 +} +.end-state-inner { + fill: ${i.compositeBackground||i.background}; + // stroke: ${i.background}; + stroke-width: 1.5 +} + +.node rect { + fill: ${i.stateBkg||i.mainBkg}; + stroke: ${i.stateBorder||i.nodeBorder}; + stroke-width: 1px; +} +.node polygon { + fill: ${i.mainBkg}; + stroke: ${i.stateBorder||i.nodeBorder};; + stroke-width: 1px; +} +#statediagram-barbEnd { + fill: ${i.lineColor}; +} + +.statediagram-cluster rect { + fill: ${i.compositeTitleBackground}; + stroke: ${i.stateBorder||i.nodeBorder}; + stroke-width: 1px; +} + +.cluster-label, .nodeLabel { + color: ${i.stateLabelColor}; +} + +.statediagram-cluster rect.outer { + rx: 5px; + ry: 5px; +} +.statediagram-state .divider { + stroke: ${i.stateBorder||i.nodeBorder}; +} + +.statediagram-state .title-state { + rx: 5px; + ry: 5px; +} +.statediagram-cluster.statediagram-cluster .inner { + fill: ${i.compositeBackground||i.background}; +} +.statediagram-cluster.statediagram-cluster-alt .inner { + fill: ${i.altBackground?i.altBackground:"#efefef"}; +} + +.statediagram-cluster .inner { + rx:0; + ry:0; +} + +.statediagram-state rect.basic { + rx: 5px; + ry: 5px; +} +.statediagram-state rect.divider { + stroke-dasharray: 10,10; + fill: ${i.altBackground?i.altBackground:"#efefef"}; +} + +.note-edge { + stroke-dasharray: 5; +} + +.statediagram-note rect { + fill: ${i.noteBkgColor}; + stroke: ${i.noteBorderColor}; + stroke-width: 1px; + rx: 0; + ry: 0; +} +.statediagram-note rect { + fill: ${i.noteBkgColor}; + stroke: ${i.noteBorderColor}; + stroke-width: 1px; + rx: 0; + ry: 0; +} + +.statediagram-note text { + fill: ${i.noteTextColor}; +} + +.statediagram-note .nodeLabel { + color: ${i.noteTextColor}; +} +.statediagram .edgeLabel { + color: red; // ${i.noteTextColor}; +} + +#dependencyStart, #dependencyEnd { + fill: ${i.lineColor}; + stroke: ${i.lineColor}; + stroke-width: 1; +} + +.statediagramTitleText { + text-anchor: middle; + font-size: 18px; + fill: ${i.textColor}; +} +`,Rgt={},iUe=(i,a)=>{Rgt[i]=a},sUe=i=>Rgt[i],bjt=()=>Object.keys(Rgt),aUe={get:sUe,set:iUe,keys:bjt,size:()=>bjt().length},oUe=i=>i.append("circle").attr("class","start-state").attr("r",Oe().state.sizeUnit).attr("cx",Oe().state.padding+Oe().state.sizeUnit).attr("cy",Oe().state.padding+Oe().state.sizeUnit),cUe=i=>i.append("line").style("stroke","grey").style("stroke-dasharray","3").attr("x1",Oe().state.textHeight).attr("class","divider").attr("x2",Oe().state.textHeight*2).attr("y1",0).attr("y2",0),uUe=(i,a)=>{const f=i.append("text").attr("x",2*Oe().state.padding).attr("y",Oe().state.textHeight+2*Oe().state.padding).attr("font-size",Oe().state.fontSize).attr("class","state-title").text(a.id),p=f.node().getBBox();return i.insert("rect",":first-child").attr("x",Oe().state.padding).attr("y",Oe().state.padding).attr("width",p.width+2*Oe().state.padding).attr("height",p.height+2*Oe().state.padding).attr("rx",Oe().state.radius),f},lUe=(i,a)=>{const f=function(N,R,z){const W=N.append("tspan").attr("x",2*Oe().state.padding).text(R);z||W.attr("dy",Oe().state.textHeight)},w=i.append("text").attr("x",2*Oe().state.padding).attr("y",Oe().state.textHeight+1.3*Oe().state.padding).attr("font-size",Oe().state.fontSize).attr("class","state-title").text(a.descriptions[0]).node().getBBox(),m=w.height,b=i.append("text").attr("x",Oe().state.padding).attr("y",m+Oe().state.padding*.4+Oe().state.dividerMargin+Oe().state.textHeight).attr("class","state-description");let E=!0,_=!0;a.descriptions.forEach(function(N){E||(f(b,N,_),_=!1),E=!1});const A=i.append("line").attr("x1",Oe().state.padding).attr("y1",Oe().state.padding+m+Oe().state.dividerMargin/2).attr("y2",Oe().state.padding+m+Oe().state.dividerMargin/2).attr("class","descr-divider"),I=b.node().getBBox(),B=Math.max(I.width,w.width);return A.attr("x2",B+3*Oe().state.padding),i.insert("rect",":first-child").attr("x",Oe().state.padding).attr("y",Oe().state.padding).attr("width",B+2*Oe().state.padding).attr("height",I.height+m+2*Oe().state.padding).attr("rx",Oe().state.radius),i},hUe=(i,a,f)=>{const p=Oe().state.padding,w=2*Oe().state.padding,m=i.node().getBBox(),b=m.width,E=m.x,_=i.append("text").attr("x",0).attr("y",Oe().state.titleShift).attr("font-size",Oe().state.fontSize).attr("class","state-title").text(a.id),I=_.node().getBBox().width+w;let B=Math.max(I,b);B===b&&(B=B+w);let N;const R=i.node().getBBox();a.doc,N=E-p,I>b&&(N=(b-B)/2+p),Math.abs(E-R.x)b&&(N=E-(I-b)/2);const z=1-Oe().state.textHeight;return i.insert("rect",":first-child").attr("x",N).attr("y",z).attr("class",f?"alt-composit":"composit").attr("width",B).attr("height",R.height+Oe().state.textHeight+Oe().state.titleShift+1).attr("rx","0"),_.attr("x",N+p),I<=b&&_.attr("x",E+(B-w)/2-I/2+p),i.insert("rect",":first-child").attr("x",N).attr("y",Oe().state.titleShift-Oe().state.textHeight-Oe().state.padding).attr("width",B).attr("height",Oe().state.textHeight*3).attr("rx",Oe().state.radius),i.insert("rect",":first-child").attr("x",N).attr("y",Oe().state.titleShift-Oe().state.textHeight-Oe().state.padding).attr("width",B).attr("height",R.height+3+2*Oe().state.textHeight).attr("rx",Oe().state.radius),i},fUe=i=>(i.append("circle").attr("class","end-state-outer").attr("r",Oe().state.sizeUnit+Oe().state.miniPadding).attr("cx",Oe().state.padding+Oe().state.sizeUnit+Oe().state.miniPadding).attr("cy",Oe().state.padding+Oe().state.sizeUnit+Oe().state.miniPadding),i.append("circle").attr("class","end-state-inner").attr("r",Oe().state.sizeUnit).attr("cx",Oe().state.padding+Oe().state.sizeUnit+2).attr("cy",Oe().state.padding+Oe().state.sizeUnit+2)),dUe=(i,a)=>{let f=Oe().state.forkWidth,p=Oe().state.forkHeight;if(a.parentId){let w=f;f=p,p=w}return i.append("rect").style("stroke","black").style("fill","black").attr("width",f).attr("height",p).attr("x",Oe().state.padding).attr("y",Oe().state.padding)},gUe=(i,a,f,p)=>{let w=0;const m=p.append("text");m.style("text-anchor","start"),m.attr("class","noteText");let b=i.replace(/\r\n/g,"
");b=b.replace(/\n/g,"
");const E=b.split(Kr.lineBreakRegex);let _=1.25*Oe().state.noteMargin;for(const A of E){const I=A.trim();if(I.length>0){const B=m.append("tspan");if(B.text(I),_===0){const N=B.node().getBBox();_+=N.height}w+=_,B.attr("x",a+Oe().state.noteMargin),B.attr("y",f+w+1.25*Oe().state.noteMargin)}}return{textWidth:m.node().getBBox().width,textHeight:w}},pUe=(i,a)=>{a.attr("class","state-note");const f=a.append("rect").attr("x",0).attr("y",Oe().state.padding),p=a.append("g"),{textWidth:w,textHeight:m}=gUe(i,0,0,p);return f.attr("height",m+2*Oe().state.noteMargin),f.attr("width",w+Oe().state.noteMargin*2),f},wjt=function(i,a){const 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E="";if(Oe().state.arrowMarkerAbsolute&&(E=window.location.protocol+"//"+window.location.host+window.location.pathname+window.location.search,E=E.replace(/\(/g,"\\("),E=E.replace(/\)/g,"\\)")),b.attr("marker-end","url("+E+"#"+p($5.relationType.DEPENDENCY)+"End)"),f.title!==void 0){const _=i.append("g").attr("class","stateLabel"),{x:A,y:I}=$a.calcLabelPosition(a.points),B=Kr.getRows(f.title);let N=0;const R=[];let z=0,W=0;for(let at=0;at<=B.length;at++){const bt=_.append("text").attr("text-anchor","middle").text(B[at]).attr("x",A).attr("y",I+N),mt=bt.node().getBBox();z=Math.max(z,mt.width),W=Math.min(W,mt.x),Ut.info(mt.x,A,I+N),N===0&&(N=bt.node().getBBox().height,Ut.info("Title height",N,I)),R.push(bt)}let et=N*B.length;if(B.length>1){const at=(B.length-1)*N*.5;R.forEach((bt,mt)=>bt.attr("y",I+mt*N-at)),et=N*B.length}const 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xoe(t,e,n,r,s,o,h,d,v,k,C,M,j){_t(t.Cb,88)&&gy(sl(u(t.Cb,88)),4),Qc(t,n),t.f=h,hE(t,d),dE(t,v),lE(t,k),fE(t,C),qg(t,M),gE(t,j),zg(t,!0),Rg(t,s),t.ok(o),b2(t,e),r!=null&&(t.i=null,fz(t,r))}function koe(t){var e,n;if(t.f){for(;t.n>0;){if(e=u(t.k.Xb(t.n-1),72),n=e.ak(),_t(n,99)&&u(n,18).Bb&dc&&(!t.e||n.Gj()!=j7||n.aj()!=0)&&e.dd()!=null)return!0;--t.n}return!1}else return t.n>0}function J4t(t,e,n){if(t<0)return y_(afe,lt(ct(Qn,1),De,1,5,[n,pe(t)]));if(e<0)throw it(new Fn(ofe+e));return y_("%s (%s) must not be greater than size (%s)",lt(ct(Qn,1),De,1,5,[n,pe(t),pe(e)]))}function t5t(t,e,n,r,s,o){var h,d,v,k;if(h=r-n,h<7){hhn(e,n,r,o);return}if(v=n+s,d=r+s,k=v+(d-v>>1),t5t(e,t,v,k,-s,o),t5t(e,t,k,d,-s,o),o.ue(t[k-1],t[k])<=0){for(;n=0?t.sh(o,n):M5t(t,s,n);else throw it(new Fn(lb+s.ne()+X_));else throw it(new Fn(Bde+e+Rde));else gh(t,r,s,n)}function Eoe(t){var e,n,r,s;if(n=u(t,49).qh(),n)try{if(r=null,e=_E((Pp(),Yh),sle(ghn(n))),e&&(s=e.rh(),s&&(r=s.Wk(kKe(n.e)))),r&&r!=t)return 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Awn(t,e,n){var r,s,o,h,d;for(h=t_(t,n),d=Nt(l0,Yg,10,e.length,0,1),r=0,o=h.Kc();o.Ob();)s=u(o.Pb(),11),je(Re(Q(s,(ae(),SO))))&&(d[r++]=u(Q(s,Ju),10));if(r=0;o+=n?1:-1)h=h|e.c.Sf(v,o,n,r&&!je(Re(Q(e.j,(ae(),Ov))))&&!je(Re(Q(e.j,(ae(),X4))))),h=h|e.q._f(v,o,n),h=h|Pue(t,v[o],n,r);return Fs(t.c,e),h}function xq(t,e,n){var r,s,o,h,d,v,k,C,M,j;for(C=OZt(t.j),M=0,j=C.length;M1&&(t.a=!0),Ven(u(n.b,65),Li(nc(u(e.b,65).c),fd(ia(nc(u(n.b,65).a),u(e.b,65).a),s))),WQt(t,e),Xce(t,n)}function Qce(t){var e,n,r,s,o,h,d;for(o=new S(t.a.a);o.a0&&o>0?h.p=e++:r>0?h.p=n++:o>0?h.p=s++:h.p=n++}wn(),Zs(t.j,new DL)}function Own(t){var e,n;n=null,e=u(Ne(t.g,0),17);do{if(n=e.d.i,Us(n,(ae(),$h)))return u(Q(n,$h),11).i;if(n.k!=(Vn(),Os)&&zr(new ar(lr(Ds(n).a.Kc(),new z))))e=u(Mr(new ar(lr(Ds(n).a.Kc(),new z))),17);else if(n.k!=Os)return null}while(n&&n.k!=(Vn(),Os));return n}function Pwn(t,e){var n,r,s,o,h,d,v,k,C;for(d=e.j,h=e.g,v=u(Ne(d,d.c.length-1),113),C=(An(0,d.c.length),u(d.c[0],113)),k=Ast(t,h,v,C),o=1;ok&&(v=n,C=s,k=r);e.a=C,e.c=v}function Fwn(t,e){var n,r;if(r=tD(t.b,e.b),!r)throw it(new No("Invalid hitboxes for scanline constraint calculation."));(ire(e.b,u(FZe(t.b,e.b),57))||ire(e.b,u(PZe(t.b,e.b),57)))&&(Gd(),e.b+""),t.a[e.b.f]=u(Cnt(t.b,e.b),57),n=u(Tnt(t.b,e.b),57),n&&(t.a[n.f]=e.b)}function yf(t){if(!t.a.d||!t.a.e)throw it(new No((P0(fpe),fpe.k+" must have a source and target "+(P0(a7t),a7t.k)+" specified.")));if(t.a.d==t.a.e)throw it(new No("Network simplex does not support self-loops: "+t.a+" "+t.a.d+" "+t.a.e));return _j(t.a.d.g,t.a),_j(t.a.e.b,t.a),t.a}function Nwn(t,e,n){var r,s,o,h,d,v,k;for(k=new Op(new F$t(t)),h=lt(ct(Jbe,1),h1e,11,0,[e,n]),d=0,v=h.length;dv-t.b&&dv-t.a&&d0&&++H;++j}return H}function Uwn(t,e){var n,r,s,o,h;for(h=u(Q(e,(gv(),d_t)),425),o=ei(e.b,0);o.b!=o.d.c;)if(s=u(ti(o),86),t.b[s.g]==0){switch(h.g){case 0:Cse(t,s);break;case 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e,n;n=u(Q(t,(Te(),uu)),163),e=u(Q(t,(ae(),B2)),303),n==(dh(),bb)?(Jt(t,uu,MO),Jt(t,B2,(q0(),Y4))):n==jy?(Jt(t,uu,MO),Jt(t,B2,(q0(),F6))):e==(q0(),Y4)?(Jt(t,uu,bb),Jt(t,B2,CO)):e==F6&&(Jt(t,uu,jy),Jt(t,B2,CO))}function kq(){kq=Z,jO=new jQ,Zme=bi(new Vs,(Wa(),cu),(ro(),EV)),eye=Ku(bi(new Vs,cu,DV),Io,MV),nye=uv(uv(VR(Ku(bi(new Vs,Dd,FV),Io,PV),qc),OV),NV),Jme=Ku(bi(bi(bi(new Vs,gb,CV),qc,SV),qc,u7),Io,_V),tye=Ku(bi(bi(new Vs,qc,u7),qc,kV),Io,xV)}function m_(){m_=Z,sye=bi(Ku(new Vs,(Wa(),Io),(ro(),nTt)),cu,EV),uye=uv(uv(VR(Ku(bi(new Vs,Dd,FV),Io,PV),qc),OV),NV),aye=Ku(bi(bi(bi(new Vs,gb,CV),qc,SV),qc,u7),Io,_V),cye=bi(bi(new Vs,cu,DV),Io,MV),oye=Ku(bi(bi(new Vs,qc,u7),qc,kV),Io,xV)}function evn(t,e,n,r,s){var o,h;(!Ga(e)&&e.c.i.c==e.d.i.c||!fne(Yo(lt(ct(Ws,1),ee,8,0,[s.i.n,s.n,s.a])),n))&&!Ga(e)&&(e.c==s?m8(e.a,0,new xo(n)):ri(e.a,new xo(n)),r&&!I0(t.a,n)&&(h=u(Q(e,(Te(),So)),74),h||(h=new Pu,Jt(e,So,h)),o=new xo(n),fs(h,o,h.c.b,h.c),Fs(t.a,o)))}function nvn(t){var e,n;for(n=new ar(lr(jo(t).a.Kc(),new z));zr(n);)if(e=u(Mr(n),17),e.c.i.k!=(Vn(),Ll))throw it(new R3(Kot+rI(t)+"' has its layer constraint set to FIRST, but has at least one incoming edge that does not come from a FIRST_SEPARATE node. 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nyn(t,e){var n,r,s,o,h,d;if(vr(e,"Partition midprocessing",1),s=new Uw,ls(Ri(new Tn(null,new _n(t.a,16)),new KK),new mw(s)),s.d!=0){for(d=u(Bl(ZQt((o=s.i,new Tn(null,(o||(s.i=new K3(s,s.c))).Nc()))),c2(new ke,new ce,new Xn,lt(ct(fl,1),oe,132,0,[(O1(),Ul)]))),15),r=d.Kc(),n=u(r.Pb(),19);r.Ob();)h=u(r.Pb(),19),swn(u(Ai(s,n),21),u(Ai(s,h),21)),n=h;or(e)}}function cle(t,e,n){var r,s,o,h,d,v,k,C;if(e.p==0){for(e.p=1,h=n,h||(s=new he,o=(r=u(Vf(Xa),9),new sh(r,u(ff(r,r.length),9),0)),h=new fa(s,o)),u(h.a,15).Fc(e),e.k==(Vn(),ks)&&u(h.b,21).Fc(u(Q(e,(ae(),oc)),61)),v=new S(e.j);v.a0){if(s=u(t.Ab.g,1934),e==null){for(o=0;o1)for(r=new S(s);r.an.s&&dd&&(d=s,C.c=Nt(Qn,De,1,0,5,1)),s==d&&le(C,new fa(n.c.i,n)));wn(),Zs(C,t.c),Hm(t.b,v.p,C)}}function cyn(t,e){var n,r,s,o,h,d,v,k,C;for(h=new S(e.b);h.ad&&(d=s,C.c=Nt(Qn,De,1,0,5,1)),s==d&&le(C,new fa(n.d.i,n)));wn(),Zs(C,t.c),Hm(t.f,v.p,C)}}function lle(t){Mw(t,new k2(_w(Ew(Cw(Tw(new kg,Tv),"ELK Box"),"Algorithm for packing of unconnected boxes, i.e. 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Nl(4),yy(e,ib("M",!0)),jc(e,4448,4607),jc(e,65438,65439),s=new d9(2),E2(s,t),E2(s,pA),n=new d9(2),n.$l(Yj(o,ib("L",!0))),n.$l(e),n=new Xm(3,n),n=new mvt(s,n),Vft=n,Vft}function Lyn(t){var e,n;if(e=Br(qe(t,(ui(),YS))),!qne(e,t)&&!o2(t,O7)&&((!t.a&&(t.a=new fe(rs,t,10,11)),t.a).i!=0||je(Re(qe(t,ZO)))))if(e==null||fy(e).length==0){if(!qne(Gn,t))throw n=Gr(Gr(new Ol("Unable to load default layout algorithm "),Gn)," for unconfigured node "),Nq(t,n),it(new R3(n.a))}else throw n=Gr(Gr(new Ol("Layout algorithm '"),e),"' not found for "),Nq(t,n),it(new R3(n.a))}function Eat(t){var e,n,r,s,o,h,d,v,k,C,M,j,H;if(n=t.i,e=t.n,t.b==0)for(H=n.c+e.b,j=n.b-e.b-e.c,h=t.a,v=0,C=h.length;v0&&(M-=r[0]+t.c,r[0]+=t.c),r[2]>0&&(M-=r[2]+t.c),r[1]=b.Math.max(r[1],M),Xj(t.a[1],n.c+e.b+r[0]-(r[1]-M)/2,r[1]);for(o=t.a,d=0,k=o.length;d0?(t.n.c.length-1)*t.i:0,r=new S(t.n);r.a1)for(r=ei(s,0);r.b!=r.d.c;)for(n=u(ti(r),231),o=0,v=new 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4:s=t.i.o.b,s>0&&(k=t.n.b/s)}Jt(t,(ae(),Fv),k)}if(v=t.o,h=t.a,r)h.a=r.a,h.b=r.b,t.d=!0;else if(e!=G1&&e!=Tb&&d!=Zo)switch(d.g){case 1:h.a=v.a/2;break;case 2:h.a=v.a,h.b=v.b/2;break;case 3:h.a=v.a/2,h.b=v.b;break;case 4:h.b=v.b/2}else h.a=v.a/2,h.b=v.b/2}function A_(t){var e,n,r,s,o,h,d,v,k,C;if(t.ej())if(C=t.Vi(),v=t.fj(),C>0)if(e=new gyt(t.Gi()),n=C,o=n<100?null:new Dp(n),VM(t,n,e.g),s=n==1?t.Zi(4,At(e,0),null,0,v):t.Zi(6,e,null,-1,v),t.bj()){for(r=new nr(e);r.e!=r.i.gc();)o=t.dj(dr(r),o);o?(o.Ei(s),o.Fi()):t.$i(s)}else o?(o.Ei(s),o.Fi()):t.$i(s);else VM(t,t.Vi(),t.Wi()),t.$i(t.Zi(6,(wn(),io),null,-1,v));else if(t.bj())if(C=t.Vi(),C>0){for(d=t.Wi(),k=C,VM(t,C,d),o=k<100?null:new Dp(k),r=0;rt.d[h.p]&&(n+=fmt(t.b,o)*u(v.b,19).a,Up(t.a,pe(o)));for(;!BC(t.a);)Hmt(t.b,u(Hx(t.a),19).a)}return n}function W3n(t,e,n,r){var s,o,h,d,v,k,C,M,j,H,G,K,tt;for(M=new xo(u(qe(t,(fq(),OSt)),8)),M.a=b.Math.max(M.a-n.b-n.c,0),M.b=b.Math.max(M.b-n.d-n.a,0),s=ye(qe(t,MSt)),(s==null||(On(s),s<=0))&&(s=1.3),d=new he,G=new nr((!t.a&&(t.a=new fe(rs,t,10,11)),t.a));G.e!=G.i.gc();)H=u(dr(G),33),h=new LWt(H),d.c[d.c.length]=h;switch(j=u(qe(t,lft),311),j.g){case 3:tt=pyn(d,e,M.a,M.b,(k=r,On(s),k));break;case 1:tt=zyn(d,e,M.a,M.b,(C=r,On(s),C));break;default:tt=X3n(d,e,M.a,M.b,(v=r,On(s),v))}o=new rz(tt),K=zat(o,e,n,M.a,M.b,r,(On(s),s)),wv(t,K.a,K.b,!1,!0)}function Y3n(t,e){var n,r,s,o;n=e.b,o=new Bu(n.j),s=0,r=n.j,r.c=Nt(Qn,De,1,0,5,1),$w(u(h2(t.b,(ve(),Pn),(nv(),Dv)),15),n),s=nI(o,s,new jX,r),$w(u(h2(t.b,Pn,pb),15),n),s=nI(o,s,new VT,r),$w(u(h2(t.b,Pn,Mv),15),n),$w(u(h2(t.b,Hn,Dv),15),n),$w(u(h2(t.b,Hn,pb),15),n),s=nI(o,s,new PN,r),$w(u(h2(t.b,Hn,Mv),15),n),$w(u(h2(t.b,mr,Dv),15),n),s=nI(o,s,new FN,r),$w(u(h2(t.b,mr,pb),15),n),s=nI(o,s,new NN,r),$w(u(h2(t.b,mr,Mv),15),n),$w(u(h2(t.b,Bn,Dv),15),n),s=nI(o,s,new qX,r),$w(u(h2(t.b,Bn,pb),15),n),$w(u(h2(t.b,Bn,Mv),15),n)}function K3n(t,e){var n,r,s,o,h,d,v,k,C,M,j,H,G,K;for(vr(e,"Layer size calculation",1),C=as,k=Cs,s=!1,d=new S(t.b);d.a.5?gt-=h*2*(G-.5):G<.5&&(gt+=o*2*(.5-G)),s=d.d.b,gttt.a-K-C&&(gt=tt.a-K-C),d.n.a=e+gt}}function X3n(t,e,n,r,s){var o,h,d,v,k,C,M,j,H,G,K,tt;for(d=Nt(aa,vo,25,t.c.length,15,1),j=new n$(new sB),e4t(j,t),k=0,K=new he;j.b.c.length!=0;)if(h=u(j.b.c.length==0?null:Ne(j.b,0),157),k>1&&Ru(h)*El(h)/2>d[0]){for(o=0;od[o];)++o;G=new Qd(K,0,o+1),M=new rz(G),C=Ru(h)/El(h),v=zat(M,e,new Cx,n,r,s,C),Li(Gf(M.e),v),R8(xE(j,M)),H=new Qd(K,o+1,K.c.length),e4t(j,H),K.c=Nt(Qn,De,1,0,5,1),k=0,AKt(d,d.length,0)}else tt=j.b.c.length==0?null:Ne(j.b,0),tt!=null&&vit(j,0),k>0&&(d[k]=d[k-1]),d[k]+=Ru(h)*El(h),++k,K.c[K.c.length]=h;return K}function Q3n(t){var e,n,r,s,o;if(r=u(Q(t,(Te(),uu)),163),r==(dh(),bb)){for(n=new ar(lr(jo(t).a.Kc(),new z));zr(n);)if(e=u(Mr(n),17),!jJt(e))throw it(new R3(Kot+rI(t)+"' has its layer constraint set to 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FIRST_SEPARATE nodes must not have incoming edges."))}else if(r==jy){for(o=new ar(lr(Ds(t).a.Kc(),new z));zr(o);)if(s=u(Mr(o),17),!jJt(s))throw it(new R3(Kot+rI(t)+"' has its layer constraint set to LAST_SEPARATE, but has at least one outgoing edge. 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f4n(t){t.b=null,t.bb=null,t.fb=null,t.qb=null,t.a=null,t.c=null,t.d=null,t.e=null,t.f=null,t.n=null,t.M=null,t.L=null,t.Q=null,t.R=null,t.K=null,t.db=null,t.eb=null,t.g=null,t.i=null,t.j=null,t.k=null,t.gb=null,t.o=null,t.p=null,t.q=null,t.r=null,t.$=null,t.ib=null,t.S=null,t.T=null,t.t=null,t.s=null,t.u=null,t.v=null,t.w=null,t.B=null,t.A=null,t.C=null,t.D=null,t.F=null,t.G=null,t.H=null,t.I=null,t.J=null,t.P=null,t.Z=null,t.U=null,t.V=null,t.W=null,t.X=null,t.Y=null,t._=null,t.ab=null,t.cb=null,t.hb=null,t.nb=null,t.lb=null,t.mb=null,t.ob=null,t.pb=null,t.jb=null,t.kb=null,t.N=!1,t.O=!1}function d4n(t,e,n){var r,s,o,h;for(vr(n,"Graph transformation ("+t.a+")",1),h=Ww(e.a),o=new S(e.b);o.a0&&(t.a=v+(H-1)*o,e.c.b+=t.a,e.f.b+=t.a)),G.a.gc()!=0&&(j=new ert(1,o),H=Txt(j,e,G,K,e.f.b+v-e.c.b),H>0&&(e.f.b+=v+(H-1)*o))}function OE(t,e){var n,r,s,o;o=t.F,e==null?(t.F=null,aE(t,null)):(t.F=(On(e),e),r=hd(e,Cu(60)),r!=-1?(s=e.substr(0,r),hd(e,Cu(46))==-1&&!hn(s,b6)&&!hn(s,tS)&&!hn(s,FH)&&!hn(s,eS)&&!hn(s,nS)&&!hn(s,rS)&&!hn(s,iS)&&!hn(s,sS)&&(s=$0e),n=Tj(e,Cu(62)),n!=-1&&(s+=""+e.substr(n+1)),aE(t,s)):(s=e,hd(e,Cu(46))==-1&&(r=hd(e,Cu(91)),r!=-1&&(s=e.substr(0,r)),!hn(s,b6)&&!hn(s,tS)&&!hn(s,FH)&&!hn(s,eS)&&!hn(s,nS)&&!hn(s,rS)&&!hn(s,iS)&&!hn(s,sS)?(s=$0e,r!=-1&&(s+=""+e.substr(r))):s=e),aE(t,s),s==e&&(t.F=t.D))),t.Db&4&&!(t.Db&1)&&mi(t,new Js(t,1,5,o,e))}function p4n(t,e){var n,r,s,o,h,d,v,k,C,M,j,H,G,K,tt,gt,Mt,St;if(K=e.b.c.length,!(K<3)){for(H=Nt(Cr,Xr,25,K,15,1),M=0,C=new S(e.b);C.ah)&&Fs(t.b,u(tt.b,17));++d}o=h}}}function xxt(t,e){var n;if(e==null||hn(e,_u)||e.length==0&&t.k!=(Ug(),U6))return null;switch(t.k.g){case 1:return Vz(e,XE)?(Nn(),r7):Vz(e,Vct)?(Nn(),F2):null;case 2:try{return pe(ql(e,Sa,wi))}catch(r){if(r=Wi(r),_t(r,127))return null;throw it(r)}case 4:try{return dy(e)}catch(r){if(r=Wi(r),_t(r,127))return 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n,r,s,o,h,d,v,k,C,M,j,H;if(n=u(po(t.b,e),124),v=u(u(Ai(t.r,e),21),84),v.dc()){n.n.d=0,n.n.a=0;return}for(k=t.u.Hc((Zu(),sg)),h=0,t.A.Hc((Al(),K2))&&Bue(t,e),d=v.Kc(),C=null,j=0,M=0;d.Ob();)r=u(d.Pb(),111),o=Xt(ye(r.b.We((Cj(),uV)))),s=r.b.rf().b,C?(H=M+C.d.a+t.w+r.d.d,h=b.Math.max(h,(k1(),wf(B1),b.Math.abs(j-o)<=B1||j==o||isNaN(j)&&isNaN(o)?0:H/(o-j)))):t.C&&t.C.d>0&&(h=b.Math.max(h,Mne(t.C.d+r.d.d,o))),C=r,j=o,M=s;t.C&&t.C.a>0&&(H=M+t.C.a,k&&(H+=C.d.a),h=b.Math.max(h,(k1(),wf(B1),b.Math.abs(j-1)<=B1||j==1||isNaN(j)&&isNaN(1)?0:H/(1-j)))),n.n.d=0,n.a.b=h}function she(t,e,n){var r,s,o,h,d,v;for(this.g=t,d=e.d.length,v=n.d.length,this.d=Nt(l0,Yg,10,d+v,0,1),h=0;h0?lit(this,this.f/this.a):E1(e.g,e.d[0]).a!=null&&E1(n.g,n.d[0]).a!=null?lit(this,(Xt(E1(e.g,e.d[0]).a)+Xt(E1(n.g,n.d[0]).a))/2):E1(e.g,e.d[0]).a!=null?lit(this,E1(e.g,e.d[0]).a):E1(n.g,n.d[0]).a!=null&&lit(this,E1(n.g,n.d[0]).a)}function w4n(t,e){var n,r,s,o,h,d,v,k,C,M;for(t.a=new dXt(Ucn(XS)),r=new S(e.a);r.a=1&&(tt-h>0&&M>=0?(v.n.a+=K,v.n.b+=o*h):tt-h<0&&C>=0&&(v.n.a+=K*tt,v.n.b+=o));t.o.a=e.a,t.o.b=e.b,Jt(t,(Te(),$2),(Al(),r=u(Vf(rA),9),new sh(r,u(ff(r,r.length),9),0)))}function x4n(t,e,n,r,s,o){var h;if(!(e==null||!tst(e,nLt,rLt)))throw it(new Fn("invalid scheme: "+e));if(!t&&!(n!=null&&hd(n,Cu(35))==-1&&n.length>0&&(Rr(0,n.length),n.charCodeAt(0)!=47)))throw it(new Fn("invalid opaquePart: "+n));if(t&&!(e!=null&&yM(gU,e.toLowerCase()))&&!(n==null||!tst(n,oA,cA)))throw it(new Fn(S0e+n));if(t&&e!=null&&yM(gU,e.toLowerCase())&&!g0n(n))throw it(new Fn(S0e+n));if(!vhn(r))throw it(new Fn("invalid device: "+r));if(!hln(s))throw h=s==null?"invalid segments: null":"invalid segment: "+oln(s),it(new Fn(h));if(!(o==null||hd(o,Cu(35))==-1))throw it(new Fn("invalid query: "+o))}function k4n(t,e){var n,r,s,o,h,d,v,k,C,M,j,H,G,K,tt,gt;for(vr(e,"Calculate Graph Size",1),e.n&&t&&gf(e,pf(t),(Sl(),Ql)),d=VE,v=VE,o=Ukt,h=Ukt,M=new nr((!t.a&&(t.a=new 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null;if(M=t.length*8,M==0)return"";for(d=M%24,H=M/24|0,j=d!=0?H+1:H,o=null,o=Nt(xh,yd,25,j*4,15,1),k=0,C=0,e=0,n=0,r=0,h=0,s=0,v=0;v>24,k=(e&3)<<24>>24,G=e&-128?(e>>2^192)<<24>>24:e>>2<<24>>24,K=n&-128?(n>>4^240)<<24>>24:n>>4<<24>>24,tt=r&-128?(r>>6^252)<<24>>24:r>>6<<24>>24,o[h++]=lp[G],o[h++]=lp[K|k<<4],o[h++]=lp[C<<2|tt],o[h++]=lp[r&63];return d==8?(e=t[s],k=(e&3)<<24>>24,G=e&-128?(e>>2^192)<<24>>24:e>>2<<24>>24,o[h++]=lp[G],o[h++]=lp[k<<4],o[h++]=61,o[h++]=61):d==16&&(e=t[s],n=t[s+1],C=(n&15)<<24>>24,k=(e&3)<<24>>24,G=e&-128?(e>>2^192)<<24>>24:e>>2<<24>>24,K=n&-128?(n>>4^240)<<24>>24:n>>4<<24>>24,o[h++]=lp[G],o[h++]=lp[K|k<<4],o[h++]=lp[C<<2],o[h++]=61),Mh(o,0,o.length)}function F5n(t,e){var n,r,s,o,h,d,v;if(t.e==0&&t.p>0&&(t.p=-(t.p-1)),t.p>Sa&&umt(e,t.p-ab),h=e.q.getDate(),oD(e,1),t.k>=0&&win(e,t.k),t.c>=0?oD(e,t.c):t.k>=0?(v=new 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S(e.a);C.a0&&le(t.p,C),le(t.o,C);e-=r,H=v+e,k+=e*t.e,ch(t.a,d,pe(H)),ch(t.b,d,k),t.j=b.Math.max(t.j,H),t.k=b.Math.max(t.k,k),t.d+=e,e+=K}}function ve(){ve=Z;var t;Zo=new NM(N_,0),Pn=new NM(Kq,1),Hn=new NM(Iot,2),mr=new NM(Oot,3),Bn=new NM(Pot,4),U1=(wn(),new s8((t=u(Vf(Xa),9),new sh(t,u(ff(t,t.length),9),0)))),Mf=jg(ji(Pn,lt(ct(Xa,1),xc,61,0,[]))),mh=jg(ji(Hn,lt(ct(Xa,1),xc,61,0,[]))),Kl=jg(ji(mr,lt(ct(Xa,1),xc,61,0,[]))),Vh=jg(ji(Bn,lt(ct(Xa,1),xc,61,0,[]))),Au=jg(ji(Pn,lt(ct(Xa,1),xc,61,0,[mr]))),lu=jg(ji(Hn,lt(ct(Xa,1),xc,61,0,[Bn]))),Df=jg(ji(Pn,lt(ct(Xa,1),xc,61,0,[Bn]))),el=jg(ji(Pn,lt(ct(Xa,1),xc,61,0,[Hn]))),Xl=jg(ji(mr,lt(ct(Xa,1),xc,61,0,[Bn]))),yh=jg(ji(Hn,lt(ct(Xa,1),xc,61,0,[mr]))),nl=jg(ji(Pn,lt(ct(Xa,1),xc,61,0,[Hn,Bn]))),Su=jg(ji(Hn,lt(ct(Xa,1),xc,61,0,[mr,Bn]))),Lu=jg(ji(Pn,lt(ct(Xa,1),xc,61,0,[mr,Bn]))),Vu=jg(ji(Pn,lt(ct(Xa,1),xc,61,0,[Hn,mr]))),Uc=jg(ji(Pn,lt(ct(Xa,1),xc,61,0,[Hn,mr,Bn])))}function Bhe(t,e){var 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xxn(t){var e,n,r,s,o,h,d,v,k,C,M,j,H,G,K,tt;for(K=new he,j=new S(t.d.b);j.as.d.d+s.d.a?C.f.d=!0:(C.f.d=!0,C.f.a=!0))),r.b!=r.d.c&&(e=n);C&&(o=u(tr(t.f,h.d.i),57),e.bo.d.d+o.d.a?C.f.d=!0:(C.f.d=!0,C.f.a=!0))}for(d=new ar(lr(jo(H).a.Kc(),new z));zr(d);)h=u(Mr(d),17),h.a.b!=0&&(e=u(Aj(h.a),8),h.d.j==(ve(),Pn)&&(tt=new T_(e,new $e(e.a,s.d.d),s,h),tt.f.a=!0,tt.a=h.d,K.c[K.c.length]=tt),h.d.j==mr&&(tt=new T_(e,new $e(e.a,s.d.d+s.d.a),s,h),tt.f.d=!0,tt.a=h.d,K.c[K.c.length]=tt))}return K}function kxn(t,e,n){var r,s,o,h,d,v,k,C,M;if(vr(n,"Network simplex node placement",1),t.e=e,t.n=u(Q(e,(ae(),Q4)),304),j3n(t),m0n(t),ls(Wo(new Tn(null,new _n(t.e.b,16)),new EQ),new q$t(t)),ls(Ri(Wo(Ri(Wo(new Tn(null,new _n(t.e.b,16)),new WT),new OQ),new PQ),new FQ),new z$t(t)),je(Re(Q(t.e,(Te(),SS))))&&(h=Rc(n,1),vr(h,"Straight Edges Pre-Processing",1),i5n(t),or(h)),t1n(t.f),o=u(Q(e,MS),19).a*t.f.a.c.length,mat(abt(obt(Mnt(t.f),o),!1),Rc(n,1)),t.d.a.gc()!=0){for(h=Rc(n,1),vr(h,"Flexible Where Space 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for(C=k;C<=s;C++)e.a[Rt.p]==Rt&&(gt=u(M.Xb(C),46),tt=u(gt.a,10),!I0(n,gt.b)&&H=G&&(Mt>G&&(H.c=Nt(Qn,De,1,0,5,1),G=Mt),H.c[H.c.length]=h);H.c.length!=0&&(j=u(Ne(H,Zz(e,H.c.length)),128),zn.a.Bc(j)!=null,j.s=K++,A5t(j,Qe,ue),H.c=Nt(Qn,De,1,0,5,1))}for(Rt=t.c.length+1,d=new S(t);d.aRn.s&&(Cl(n),mu(Rn.i,r),r.c>0&&(r.a=Rn,le(Rn.t,r),r.b=_e,le(_e.i,r)))}function Ixt(t){var e,n,r,s,o;switch(e=t.c,e){case 11:return t.Ml();case 12:return t.Ol();case 14:return t.Ql();case 15:return t.Tl();case 16:return t.Rl();case 17:return t.Ul();case 21:return fi(t),gi(),gi(),pA;case 10:switch(t.a){case 65:return t.yl();case 90:return t.Dl();case 122:return t.Kl();case 98:return t.El();case 66:return t.zl();case 60:return t.Jl();case 62:return t.Hl()}}switch(o=vxn(t),e=t.c,e){case 3:return t.Zl(o);case 4:return t.Xl(o);case 5:return t.Yl(o);case 0:if(t.a==123&&t.d=48&&e<=57){for(r=e-48;s=48&&e<=57;)if(r=r*10+e-48,r<0)throw it(new Nr(qr((Pr(),N8t))))}else throw it(new Nr(qr((Pr(),v0e))));if(n=r,e==44){if(s>=t.j)throw it(new Nr(qr((Pr(),y0e))));if((e=wa(t.i,s++))>=48&&e<=57){for(n=e-48;s=48&&e<=57;)if(n=n*10+e-48,n<0)throw it(new Nr(qr((Pr(),N8t))));if(r>n)throw it(new Nr(qr((Pr(),x0e))))}else n=-1}if(e!=125)throw it(new Nr(qr((Pr(),m0e))));t.sl(s)?(o=(gi(),gi(),new Xm(9,o)),t.d=s+1):(o=(gi(),gi(),new Xm(3,o)),t.d=s),o.dm(r),o.cm(n),fi(t)}}return o}function Xhe(t,e,n,r,s){var o,h,d,v,k,C,M,j,H,G,K,tt,gt,Mt,St,Rt,Kt,ue,_e,We,Qe,Rn,zn;for(K=new Xc(e.b),Rt=new Xc(e.b),j=new Xc(e.b),We=new Xc(e.b),tt=new Xc(e.b),_e=ei(e,0);_e.b!=_e.d.c;)for(Kt=u(ti(_e),11),d=new S(Kt.g);d.a0,gt=Kt.g.c.length>0,k&>?j.c[j.c.length]=Kt:k?K.c[K.c.length]=Kt:gt&&(Rt.c[Rt.c.length]=Kt);for(G=new S(K);G.a1)for(G=new Nx((!t.a&&(t.a=new fe(Ji,t,6,6)),t.a));G.e!=G.i.gc();)f_(G);for(h=u(At((!t.a&&(t.a=new fe(Ji,t,6,6)),t.a),0),202),tt=pi,pi>Kt+Rt?tt=Kt+Rt:piue+K?gt=ue+K:jsKt-Rt&&ttue-K&>pi+hr?We=pi+hr:Ktjs+_e?Qe=js+_e:uepi-hr&&Wejs-_e&&Qen&&(j=n-1),H=xP+ul(e,24)*$I*M-M/2,H<0?H=1:H>r&&(H=r-1),s=(Sw(),v=new xp,v),iz(s,j),sz(s,H),Dr((!h.a&&(h.a=new As(Gh,h,5)),h.a),s)}function Te(){Te=Z,lht=(ui(),p4e),y9t=b4e,OO=hAt,Tf=w4e,V6=fAt,jv=v4e,Wy=dAt,S7=gAt,A7=pAt,hht=JG,$v=W2,fht=m4e,LS=vAt,bG=K6,IO=(Fxt(),fve),J4=dve,q2=gve,t5=pve,Zve=new eo(ZG,pe(0)),_7=uve,m9t=lve,H6=hve,A9t=Bve,x9t=vve,k9t=xve,ght=Ave,E9t=Tve,T9t=_ve,wG=zve,pht=Rve,_9t=Ove,C9t=Dve,S9t=Fve,Bv=rve,AS=ive,sht=xwe,QCt=Ewe,g9t=new Ow(12),d9t=new eo(U2,g9t),YCt=(W0(),N7),eg=new eo(zSt,YCt),Vy=new eo(dl,0),Jve=new eo(Eft,pe(1)),rG=new eo(W6,GE),z2=QG,cs=KS,C7=u5,Gve=QO,Id=a4e,qy=s5,tme=new eo(Tft,(Nn(),!0)),Hy=ZO,j2=bft,$2=G2,pG=xb,uht=XG,WCt=(ao(),h0),Wl=new eo(qv,WCt),Nv=o5,dG=XSt,Gy=Qy,Qve=kft,w9t=uAt,b9t=(l4(),iP),new eo(iAt,b9t),Yve=vft,Kve=mft,Xve=yft,Wve=wft,dht=wve,c9t=Gwe,oht=Vwe,MS=bve,uu=Bwe,zy=dwe,_S=fwe,$y=J2e,VCt=twe,eht=iwe,DO=ewe,nht=lwe,u9t=Uwe,l9t=Wwe,r9t=Dwe,gG=ove,cht=Xwe,aht=_we,f9t=eve,XCt=mwe,iht=ywe,tht=YG,h9t=Ywe,sG=U2e,zCt=G2e,iG=V2e,t9t=Lwe,JCt=Awe,e9t=Mwe,E7=c5,So=a5,Jg=HSt,Od=pft,rht=gft,GCt=awe,tp=xft,CS=u4e,lG=l4e,Rv=aAt,p9t=h4e,T7=f4e,s9t=jwe,a9t=zwe,Uy=Y6,Zlt=H2e,o9t=Hwe,uG=bwe,cG=pwe,fG=JO,i9t=Pwe,SS=Zwe,PO=bAt,UCt=gwe,v9t=cve,KCt=wwe,Uve=Nwe,Vve=cwe,n9t=WSt,hG=Rwe,oG=uwe,wb=Z2e,HCt=X2e,aG=Y2e,qCt=K2e,Jlt=Q2e,q6=W2e,ZCt=Swe}function Hat(t,e){Lat();var n,r,s,o,h,d,v,k,C,M,j,H,G,K,tt,gt,Mt,St,Rt,Kt,ue,_e,We,Qe,Rn,zn,hr,pi;if(We=t.e,G=t.d,s=t.a,We==0)switch(e){case 0:return"0";case 1:return $E;case 2:return"0.00";case 3:return"0.000";case 4:return"0.0000";case 5:return"0.00000";case 6:return"0.000000";default:return ue=new Mp,e<0?ue.a+="0E+":ue.a+="0E",ue.a+=-e,ue.a}if(St=G*10+1+7,Rt=Nt(xh,yd,25,St+1,15,1),n=St,G==1)if(d=s[0],d<0){pi=Ns(d,co);do K=pi,pi=aI(pi,10),Rt[--n]=48+Ar(Jp(K,_a(pi,10)))&ys;while(yc(pi,0)!=0)}else{pi=d;do K=pi,pi=pi/10|0,Rt[--n]=48+(K-pi*10)&ys;while(pi!=0)}else{Rn=Nt(Cr,Xr,25,G,15,1),hr=G,Dc(s,0,Rn,0,hr);t:for(;;){for(_e=0,k=hr-1;k>=0;k--)zn=Pa(F0(_e,32),Ns(Rn[k],co)),gt=P0n(zn),Rn[k]=Ar(gt),_e=Ar($p(gt,32));Mt=Ar(_e),tt=n;do Rt[--n]=48+Mt%10&ys;while((Mt=Mt/10|0)!=0&&n!=0);for(r=9-tt+n,v=0;v0;v++)Rt[--n]=48;for(M=hr-1;Rn[M]==0;M--)if(M==0)break t;hr=M+1}for(;Rt[n]==48;)++n}if(H=We<0,h=St-n-e-1,e==0)return H&&(Rt[--n]=45),Mh(Rt,n,St-n);if(e>0&&h>=-6){if(h>=0){for(C=n+h,j=St-1;j>=C;j--)Rt[j+1]=Rt[j];return Rt[++C]=46,H&&(Rt[--n]=45),Mh(Rt,n,St-n+1)}for(M=2;M<-h+1;M++)Rt[--n]=48;return Rt[--n]=46,Rt[--n]=48,H&&(Rt[--n]=45),Mh(Rt,n,St-n)}return Qe=n+1,o=St,Kt=new Im,H&&(Kt.a+="-"),o-Qe>=1?(qp(Kt,Rt[n]),Kt.a+=".",Kt.a+=Mh(Rt,n+1,St-n-1)):Kt.a+=Mh(Rt,n,St-n),Kt.a+="E",h>0&&(Kt.a+="+"),Kt.a+=""+h,Kt.a}function Jhe(t,e){var n,r,s,o,h,d,v,k,C,M,j,H,G,K,tt,gt,Mt,St,Rt,Kt,ue;switch(t.c=e,t.g=new _r,n=(Pm(),new Mm(t.c)),r=new er(n),p3t(r),St=Br(qe(t.c,(cI(),lSt))),v=u(qe(t.c,sft),316),Kt=u(qe(t.c,aft),429),h=u(qe(t.c,oSt),482),Rt=u(qe(t.c,ift),430),t.j=Xt(ye(qe(t.c,M3e))),d=t.a,v.g){case 0:d=t.a;break;case 1:d=t.b;break;case 2:d=t.i;break;case 3:d=t.e;break;case 4:d=t.f;break;default:throw it(new Fn(_H+(v.f!=null?v.f:""+v.g)))}if(t.d=new EQt(d,Kt,h),Jt(t.d,(Z8(),fS),Re(qe(t.c,A3e))),t.d.c=je(Re(qe(t.c,cSt))),p$(t.c).i==0)return t.d;for(M=new nr(p$(t.c));M.e!=M.i.gc();){for(C=u(dr(M),33),H=C.g/2,j=C.f/2,ue=new $e(C.i+H,C.j+j);Tl(t.g,ue);)jm(ue,(b.Math.random()-.5)*Ed,(b.Math.random()-.5)*Ed);K=u(qe(C,(ui(),JO)),142),tt=new $Qt(ue,new ah(ue.a-H-t.j/2-K.b,ue.b-j-t.j/2-K.d,C.g+t.j+(K.b+K.c),C.f+t.j+(K.d+K.a))),le(t.d.i,tt),ki(t.g,ue,new fa(tt,C))}switch(Rt.g){case 0:if(St==null)t.d.d=u(Ne(t.d.i,0),65);else for(Mt=new S(t.d.i);Mt.a1&&fs(C,gt,C.c.b,C.c),tz(s)));gt=Mt}return C}function Mxn(t,e,n){var r,s,o,h,d,v,k,C,M,j,H,G,K,tt,gt,Mt,St,Rt,Kt,ue,_e,We,Qe,Rn,zn,hr,pi,js,Zl,Xh,K1;for(vr(n,"Greedy cycle removal",1),St=e.a,K1=St.c.length,t.a=Nt(Cr,Xr,25,K1,15,1),t.c=Nt(Cr,Xr,25,K1,15,1),t.b=Nt(Cr,Xr,25,K1,15,1),k=0,gt=new S(St);gt.a0?hr+1:1);for(h=new S(ue.g);h.a0?hr+1:1)}t.c[k]==0?ri(t.e,K):t.a[k]==0&&ri(t.f,K),++k}for(G=-1,H=1,M=new he,t.d=u(Q(e,(ae(),$6)),230);K1>0;){for(;t.e.b!=0;)js=u(Ont(t.e),10),t.b[js.p]=G--,ext(t,js),--K1;for(;t.f.b!=0;)Zl=u(Ont(t.f),10),t.b[Zl.p]=H++,ext(t,Zl),--K1;if(K1>0){for(j=Sa,Mt=new S(St);Mt.a=j&&(Rt>j&&(M.c=Nt(Qn,De,1,0,5,1),j=Rt),M.c[M.c.length]=K));C=t.Zf(M),t.b[C.p]=H++,ext(t,C),--K1}}for(pi=St.c.length+1,k=0;kt.b[Xh]&&(bv(r,!0),Jt(e,_O,(Nn(),!0)));t.a=null,t.c=null,t.b=null,Ah(t.f),Ah(t.e),or(n)}function efe(t,e){var n,r,s,o,h,d,v,k,C,M,j,H,G,K,tt,gt;for(r=new he,d=new he,tt=e/2,H=t.gc(),s=u(t.Xb(0),8),gt=u(t.Xb(1),8),G=rat(s.a,s.b,gt.a,gt.b,tt),le(r,(An(0,G.c.length),u(G.c[0],8))),le(d,(An(1,G.c.length),u(G.c[1],8))),k=2;k=0;v--)ri(n,(An(v,h.c.length),u(h.c[v],8)));return n}function Dxn(t){var e,n,r,s,o,h,d,v,k,C,M,j,H;if(h=!0,M=null,r=null,s=null,e=!1,H=o5e,k=null,o=null,d=0,v=ust(t,d,nLt,rLt),v=0&&hn(t.substr(d,2),"//")?(d+=2,v=ust(t,d,oA,cA),r=t.substr(d,v-d),d=v):M!=null&&(d==t.length||(Rr(d,t.length),t.charCodeAt(d)!=47))&&(h=!1,v=O2t(t,Cu(35),d),v==-1&&(v=t.length),r=t.substr(d,v-d),d=v);if(!n&&d0&&wa(C,C.length-1)==58&&(s=C,d=v)),d=t.j){t.a=-1,t.c=1;return}if(e=wa(t.i,t.d++),t.a=e,t.b==1){switch(e){case 92:if(r=10,t.d>=t.j)throw it(new Nr(qr((Pr(),OH))));t.a=wa(t.i,t.d++);break;case 45:(t.e&512)==512&&t.d=t.j||wa(t.i,t.d)!=63)break;if(++t.d>=t.j)throw it(new Nr(qr((Pr(),out))));switch(e=wa(t.i,t.d++),e){case 58:r=13;break;case 61:r=14;break;case 33:r=15;break;case 91:r=19;break;case 62:r=18;break;case 60:if(t.d>=t.j)throw it(new Nr(qr((Pr(),out))));if(e=wa(t.i,t.d++),e==61)r=16;else if(e==33)r=17;else throw it(new Nr(qr((Pr(),t0e))));break;case 35:for(;t.d=t.j)throw it(new Nr(qr((Pr(),OH))));t.a=wa(t.i,t.d++);break;default:r=0}t.c=r}function Oxn(t){var e,n,r,s,o,h,d,v,k,C,M,j,H,G,K,tt,gt,Mt,St,Rt,Kt,ue,_e,We,Qe,Rn,zn,hr;if(_e=u(Q(t,(Te(),cs)),98),_e!=(ua(),G1)&&_e!=Tb){for(G=t.b,H=G.c.length,C=new Xc((jl(H+2,Yat),J$(Pa(Pa(5,H+2),(H+2)/10|0)))),K=new Xc((jl(H+2,Yat),J$(Pa(Pa(5,H+2),(H+2)/10|0)))),le(C,new _r),le(C,new _r),le(K,new he),le(K,new he),ue=new he,e=0;e=Kt||!tfn(gt,r))&&(r=XQt(e,C)),Eo(gt,r),o=new ar(lr(jo(gt).a.Kc(),new z));zr(o);)s=u(Mr(o),17),!t.a[s.p]&&(K=s.c.i,--t.e[K.p],t.e[K.p]==0&&R8(xE(H,K)));for(k=C.c.length-1;k>=0;--k)le(e.b,(An(k,C.c.length),u(C.c[k],29)));e.a.c=Nt(Qn,De,1,0,5,1),or(n)}function nfe(t){var e,n,r,s,o,h,d,v,k;for(t.b=1,fi(t),e=null,t.c==0&&t.a==94?(fi(t),e=(gi(),gi(),new Nl(4)),jc(e,0,e7),d=new Nl(4)):d=(gi(),gi(),new Nl(4)),s=!0;(k=t.c)!=1;){if(k==0&&t.a==93&&!s){e&&(L_(e,d),d=e);break}if(n=t.a,r=!1,k==10)switch(n){case 100:case 68:case 119:case 87:case 115:case 83:yy(d,ME(n)),r=!0;break;case 105:case 73:case 99:case 67:n=(yy(d,ME(n)),-1),n<0&&(r=!0);break;case 112:case 80:if(v=u5t(t,n),!v)throw it(new Nr(qr((Pr(),cut))));yy(d,v),r=!0;break;default:n=H5t(t)}else if(k==24&&!s){if(e&&(L_(e,d),d=e),o=nfe(t),L_(d,o),t.c!=0||t.a!=93)throw it(new Nr(qr((Pr(),l0e))));break}if(fi(t),!r){if(k==0){if(n==91)throw it(new Nr(qr((Pr(),P8t))));if(n==93)throw it(new Nr(qr((Pr(),F8t))));if(n==45&&!s&&t.a!=93)throw it(new Nr(qr((Pr(),uut))))}if(t.c!=0||t.a!=45||n==45&&s)jc(d,n,n);else{if(fi(t),(k=t.c)==1)throw it(new Nr(qr((Pr(),PH))));if(k==0&&t.a==93)jc(d,n,n),jc(d,45,45);else{if(k==0&&t.a==93||k==24)throw it(new Nr(qr((Pr(),uut))));if(h=t.a,k==0){if(h==91)throw it(new Nr(qr((Pr(),P8t))));if(h==93)throw it(new Nr(qr((Pr(),F8t))));if(h==45)throw it(new Nr(qr((Pr(),uut))))}else k==10&&(h=H5t(t));if(fi(t),n>h)throw it(new Nr(qr((Pr(),d0e))));jc(d,n,h)}}}s=!1}if(t.c==1)throw it(new Nr(qr((Pr(),PH))));return v4(d),S_(d),t.b=0,fi(t),d}function Fxn(t){Ir(t.c,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#decimal"])),Ir(t.d,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#integer"])),Ir(t.e,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#boolean"])),Ir(t.f,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"EBoolean",ci,"EBoolean:Object"])),Ir(t.i,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#byte"])),Ir(t.g,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#hexBinary"])),Ir(t.j,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"EByte",ci,"EByte:Object"])),Ir(t.n,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"EChar",ci,"EChar:Object"])),Ir(t.t,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#double"])),Ir(t.u,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"EDouble",ci,"EDouble:Object"])),Ir(t.F,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#float"])),Ir(t.G,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"EFloat",ci,"EFloat:Object"])),Ir(t.I,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#int"])),Ir(t.J,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"EInt",ci,"EInt:Object"])),Ir(t.N,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#long"])),Ir(t.O,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"ELong",ci,"ELong:Object"])),Ir(t.Z,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#short"])),Ir(t.$,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"EShort",ci,"EShort:Object"])),Ir(t._,Yr,lt(ct(Ae,1),ee,2,6,[Aa,"http://www.w3.org/2001/XMLSchema#string"]))}function Nxn(t){var e,n,r,s,o,h,d,v,k,C,M,j,H,G,K,tt,gt,Mt,St,Rt,Kt,ue,_e,We,Qe,Rn,zn,hr;if(t.c.length==1)return An(0,t.c.length),u(t.c[0],135);if(t.c.length<=0)return new j$;for(v=new S(t);v.aM&&(zn=0,hr+=C+_e,C=0),U2n(Kt,h,zn,hr),e=b.Math.max(e,zn+ue.a),C=b.Math.max(C,ue.b),zn+=ue.a+_e;for(Rt=new _r,n=new _r,Qe=new S(t);Qe.aiat(o))&&(M=o);for(!M&&(M=(An(0,tt.c.length),u(tt.c[0],180))),K=new S(e.b);K.a=-1900?1:0,n>=4?Gr(t,lt(ct(Ae,1),ee,2,6,[mfe,yfe])[d]):Gr(t,lt(ct(Ae,1),ee,2,6,["BC","AD"])[d]);break;case 121:Mfn(t,n,r);break;case 77:Pmn(t,n,r);break;case 107:v=s.q.getHours(),v==0?Jd(t,24,n):Jd(t,v,n);break;case 83:ewn(t,n,s);break;case 69:C=r.q.getDay(),n==5?Gr(t,lt(ct(Ae,1),ee,2,6,["S","M","T","W","T","F","S"])[C]):n==4?Gr(t,lt(ct(Ae,1),ee,2,6,[cot,uot,lot,hot,fot,dot,got])[C]):Gr(t,lt(ct(Ae,1),ee,2,6,["Sun","Mon","Tue","Wed","Thu","Fri","Sat"])[C]);break;case 97:s.q.getHours()>=12&&s.q.getHours()<24?Gr(t,lt(ct(Ae,1),ee,2,6,["AM","PM"])[1]):Gr(t,lt(ct(Ae,1),ee,2,6,["AM","PM"])[0]);break;case 104:M=s.q.getHours()%12,M==0?Jd(t,12,n):Jd(t,M,n);break;case 75:j=s.q.getHours()%12,Jd(t,j,n);break;case 72:H=s.q.getHours(),Jd(t,H,n);break;case 99:G=r.q.getDay(),n==5?Gr(t,lt(ct(Ae,1),ee,2,6,["S","M","T","W","T","F","S"])[G]):n==4?Gr(t,lt(ct(Ae,1),ee,2,6,[cot,uot,lot,hot,fot,dot,got])[G]):n==3?Gr(t,lt(ct(Ae,1),ee,2,6,["Sun","Mon","Tue","Wed","Thu","Fri","Sat"])[G]):Jd(t,G,1);break;case 76:K=r.q.getMonth(),n==5?Gr(t,lt(ct(Ae,1),ee,2,6,["J","F","M","A","M","J","J","A","S","O","N","D"])[K]):n==4?Gr(t,lt(ct(Ae,1),ee,2,6,[Qat,Zat,Jat,tot,w6,eot,not,rot,iot,sot,aot,oot])[K]):n==3?Gr(t,lt(ct(Ae,1),ee,2,6,["Jan","Feb","Mar","Apr",w6,"Jun","Jul","Aug","Sep","Oct","Nov","Dec"])[K]):Jd(t,K+1,n);break;case 81:tt=r.q.getMonth()/3|0,n<4?Gr(t,lt(ct(Ae,1),ee,2,6,["Q1","Q2","Q3","Q4"])[tt]):Gr(t,lt(ct(Ae,1),ee,2,6,["1st quarter","2nd quarter","3rd quarter","4th quarter"])[tt]);break;case 100:gt=r.q.getDate(),Jd(t,gt,n);break;case 109:k=s.q.getMinutes(),Jd(t,k,n);break;case 115:h=s.q.getSeconds(),Jd(t,h,n);break;case 122:n<4?Gr(t,o.c[0]):Gr(t,o.c[1]);break;case 118:Gr(t,o.b);break;case 90:n<3?Gr(t,Vpn(o)):n==3?Gr(t,Wpn(o)):Gr(t,Ypn(o.a));break;default:return!1}return!0}function Pxt(t,e,n,r){var s,o,h,d,v,k,C,M,j,H,G,K,tt,gt,Mt,St,Rt,Kt,ue,_e,We,Qe,Rn,zn,hr,pi;if(Hue(e),v=u(At((!e.b&&(e.b=new Cn(br,e,4,7)),e.b),0),82),C=u(At((!e.c&&(e.c=new Cn(br,e,5,8)),e.c),0),82),d=Do(v),k=Do(C),h=(!e.a&&(e.a=new fe(Ji,e,6,6)),e.a).i==0?null:u(At((!e.a&&(e.a=new fe(Ji,e,6,6)),e.a),0),202),_e=u(tr(t.a,d),10),zn=u(tr(t.a,k),10),We=null,hr=null,_t(v,186)&&(ue=u(tr(t.a,v),299),_t(ue,11)?We=u(ue,11):_t(ue,10)&&(_e=u(ue,10),We=u(Ne(_e.j,0),11))),_t(C,186)&&(Rn=u(tr(t.a,C),299),_t(Rn,11)?hr=u(Rn,11):_t(Rn,10)&&(zn=u(Rn,10),hr=u(Ne(zn.j,0),11))),!_e||!zn)throw it(new jC("The source or the target of edge "+e+" could not be found. This usually happens when an edge connects a node laid out by ELK Layered to a node in another level of hierarchy laid out by either another instance of ELK Layered or another layout algorithm alltogether. The former can be solved by setting the hierarchyHandling option to INCLUDE_CHILDREN."));for(K=new Vw,Mo(K,e),Jt(K,(ae(),_i),e),Jt(K,(Te(),So),null),H=u(Q(r,Vc),21),_e==zn&&H.Fc((oo(),xS)),We||(Kt=(so(),nu),Qe=null,h&&G3(u(Q(_e,cs),98))&&(Qe=new $e(h.j,h.k),JZt(Qe,cD(e)),LJt(Qe,n),ey(k,d)&&(Kt=tl,Li(Qe,_e.n))),We=zle(_e,Qe,Kt,r)),hr||(Kt=(so(),tl),pi=null,h&&G3(u(Q(zn,cs),98))&&(pi=new $e(h.b,h.c),JZt(pi,cD(e)),LJt(pi,n)),hr=zle(zn,pi,Kt,Na(zn))),Oa(K,We),oa(K,hr),(We.e.c.length>1||We.g.c.length>1||hr.e.c.length>1||hr.g.c.length>1)&&H.Fc((oo(),yS)),j=new nr((!e.n&&(e.n=new fe(qo,e,1,7)),e.n));j.e!=j.i.gc();)if(M=u(dr(j),137),!je(Re(qe(M,z2)))&&M.a)switch(tt=Vit(M),le(K.b,tt),u(Q(tt,Od),272).g){case 1:case 2:H.Fc((oo(),m7));break;case 0:H.Fc((oo(),v7)),Jt(tt,Od,(M1(),P7))}if(o=u(Q(r,_S),314),gt=u(Q(r,gG),315),s=o==(n6(),EO)||gt==(u_(),xht),h&&(!h.a&&(h.a=new As(Gh,h,5)),h.a).i!=0&&s){for(Mt=lI(h),G=new Pu,Rt=ei(Mt,0);Rt.b!=Rt.d.c;)St=u(ti(Rt),8),ri(G,new xo(St));Jt(K,aCt,G)}return K}function $xn(t){t.gb||(t.gb=!0,t.b=ic(t,0),ns(t.b,18),Fi(t.b,19),t.a=ic(t,1),ns(t.a,1),Fi(t.a,2),Fi(t.a,3),Fi(t.a,4),Fi(t.a,5),t.o=ic(t,2),ns(t.o,8),ns(t.o,9),Fi(t.o,10),Fi(t.o,11),Fi(t.o,12),Fi(t.o,13),Fi(t.o,14),Fi(t.o,15),Fi(t.o,16),Fi(t.o,17),Fi(t.o,18),Fi(t.o,19),Fi(t.o,20),Fi(t.o,21),Fi(t.o,22),Fi(t.o,23),Co(t.o),Co(t.o),Co(t.o),Co(t.o),Co(t.o),Co(t.o),Co(t.o),Co(t.o),Co(t.o),Co(t.o),t.p=ic(t,3),ns(t.p,2),ns(t.p,3),ns(t.p,4),ns(t.p,5),Fi(t.p,6),Fi(t.p,7),Co(t.p),Co(t.p),t.q=ic(t,4),ns(t.q,8),t.v=ic(t,5),Fi(t.v,9),Co(t.v),Co(t.v),Co(t.v),t.w=ic(t,6),ns(t.w,2),ns(t.w,3),ns(t.w,4),Fi(t.w,5),t.B=ic(t,7),Fi(t.B,1),Co(t.B),Co(t.B),Co(t.B),t.Q=ic(t,8),Fi(t.Q,0),Co(t.Q),t.R=ic(t,9),ns(t.R,1),t.S=ic(t,10),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),Co(t.S),t.T=ic(t,11),Fi(t.T,10),Fi(t.T,11),Fi(t.T,12),Fi(t.T,13),Fi(t.T,14),Co(t.T),Co(t.T),t.U=ic(t,12),ns(t.U,2),ns(t.U,3),Fi(t.U,4),Fi(t.U,5),Fi(t.U,6),Fi(t.U,7),Co(t.U),t.V=ic(t,13),Fi(t.V,10),t.W=ic(t,14),ns(t.W,18),ns(t.W,19),ns(t.W,20),Fi(t.W,21),Fi(t.W,22),Fi(t.W,23),t.bb=ic(t,15),ns(t.bb,10),ns(t.bb,11),ns(t.bb,12),ns(t.bb,13),ns(t.bb,14),ns(t.bb,15),ns(t.bb,16),Fi(t.bb,17),Co(t.bb),Co(t.bb),t.eb=ic(t,16),ns(t.eb,2),ns(t.eb,3),ns(t.eb,4),ns(t.eb,5),ns(t.eb,6),ns(t.eb,7),Fi(t.eb,8),Fi(t.eb,9),t.ab=ic(t,17),ns(t.ab,0),ns(t.ab,1),t.H=ic(t,18),Fi(t.H,0),Fi(t.H,1),Fi(t.H,2),Fi(t.H,3),Fi(t.H,4),Fi(t.H,5),Co(t.H),t.db=ic(t,19),Fi(t.db,2),t.c=oi(t,20),t.d=oi(t,21),t.e=oi(t,22),t.f=oi(t,23),t.i=oi(t,24),t.g=oi(t,25),t.j=oi(t,26),t.k=oi(t,27),t.n=oi(t,28),t.r=oi(t,29),t.s=oi(t,30),t.t=oi(t,31),t.u=oi(t,32),t.fb=oi(t,33),t.A=oi(t,34),t.C=oi(t,35),t.D=oi(t,36),t.F=oi(t,37),t.G=oi(t,38),t.I=oi(t,39),t.J=oi(t,40),t.L=oi(t,41),t.M=oi(t,42),t.N=oi(t,43),t.O=oi(t,44),t.P=oi(t,45),t.X=oi(t,46),t.Y=oi(t,47),t.Z=oi(t,48),t.$=oi(t,49),t._=oi(t,50),t.cb=oi(t,51),t.K=oi(t,52))}function ui(){ui=Z;var t,e;YS=new Vi(ude),O7=new Vi(lde),NSt=(t0(),uft),a4e=new mn(xkt,NSt),W6=new mn(E6,null),o4e=new Vi(p8t),RSt=(hy(),ji(fft,lt(ct(dft,1),oe,291,0,[hft]))),YG=new mn(mH,RSt),QO=new mn(JI,(Nn(),!1)),jSt=(ao(),h0),qv=new mn(Tkt,jSt),qSt=(W0(),Cft),zSt=new mn(QI,qSt),GSt=new mn(CH,!1),USt=(G0(),tU),s5=new mn(vH,USt),nAt=new Ow(12),U2=new mn(xv,nAt),KG=new mn(GI,!1),WSt=new mn(_ct,!1),tP=new mn(j_,!1),oAt=(ua(),Tb),KS=new mn(Got,oAt),Y6=new Vi(yH),ZG=new Vi(VI),Eft=new Vi(tH),Tft=new Vi(R_),YSt=new Pu,a5=new mn(Okt,YSt),u4e=new mn(Nkt,!1),l4e=new mn(Bkt,!1),KSt=new OC,JO=new mn(jkt,KSt),QG=new mn(mkt,!1),g4e=new mn(hde,1),new mn(fde,!0),pe(0),new mn(dde,pe(100)),new mn(gde,!1),pe(0),new mn(pde,pe(4e3)),pe(0),new mn(bde,pe(400)),new mn(wde,!1),new mn(vde,!1),new mn(mde,!0),new mn(yde,!1),BSt=(jz(),Lft),c4e=new mn(g8t,BSt),p4e=new mn(okt,10),b4e=new mn(ckt,10),hAt=new mn(jot,20),w4e=new mn(ukt,10),fAt=new mn(Vot,2),v4e=new mn(lkt,10),dAt=new mn(hkt,0),JG=new mn(gkt,5),gAt=new mn(fkt,1),pAt=new mn(dkt,1),W2=new mn(Cy,20),m4e=new mn(pkt,10),vAt=new mn(bkt,10),K6=new Vi(wkt),wAt=new CUt,bAt=new mn($kt,wAt),f4e=new Vi(Cct),rAt=!1,h4e=new mn(Tct,rAt),QSt=new Ow(5),XSt=new mn(Ckt,QSt),ZSt=(py(),e=u(Vf(lo),9),new sh(e,u(ff(e,e.length),9),0)),o5=new mn(UE,ZSt),sAt=(l4(),Eb),iAt=new mn(Akt,sAt),vft=new Vi(Lkt),mft=new Vi(Mkt),yft=new Vi(Dkt),wft=new Vi(Ikt),JSt=(t=u(Vf(rA),9),new sh(t,u(ff(t,t.length),9),0)),G2=new mn(D4,JSt),eAt=un((ll(),R7)),xb=new mn(T6,eAt),tAt=new $e(0,0),c5=new mn(C6,tAt),XG=new mn(Ect,!1),$St=(M1(),P7),pft=new mn(Pkt,$St),gft=new mn(eH,!1),pe(1),new mn(xde,null),aAt=new Vi(Rkt),xft=new Vi(Fkt),lAt=(ve(),Zo),u5=new mn(ykt,lAt),dl=new Vi(vkt),cAt=(Zu(),un(Cb)),Qy=new mn(WE,cAt),kft=new mn(_kt,!1),uAt=new mn(Skt,!0),ZO=new mn(kkt,!1),bft=new mn(Ekt,!1),HSt=new mn($ot,1),VSt=(hq(),Sft),new mn(kde,VSt),d4e=!0}function ae(){ae=Z;var t,e;_i=new Vi(w6t),nCt=new Vi("coordinateOrigin"),Klt=new Vi("processors"),eCt=new Ps("compoundNode",(Nn(),!1)),SO=new Ps("insideConnections",!1),aCt=new Vi("originalBendpoints"),oCt=new Vi("originalDummyNodePosition"),cCt=new Vi("originalLabelEdge"),LO=new Vi("representedLabels"),kS=new Vi("endLabels"),B6=new Vi("endLabel.origin"),j6=new Ps("labelSide",(zl(),rP)),K4=new Ps("maxEdgeThickness",0),q1=new Ps("reversed",!1),$6=new Vi(i1e),r1=new Ps("longEdgeSource",null),$h=new Ps("longEdgeTarget",null),Ry=new Ps("longEdgeHasLabelDummies",!1),AO=new Ps("longEdgeBeforeLabelDummy",!1),tG=new Ps("edgeConstraint",(d2(),Ilt)),Pv=new Vi("inLayerLayoutUnit"),B2=new Ps("inLayerConstraint",(q0(),CO)),R6=new Ps("inLayerSuccessorConstraint",new he),sCt=new Ps("inLayerSuccessorConstraintBetweenNonDummies",!1),Ju=new Vi("portDummy"),JV=new Ps("crossingHint",pe(0)),Vc=new Ps("graphProperties",(e=u(Vf(jlt),9),new sh(e,u(ff(e,e.length),9),0))),oc=new Ps("externalPortSide",(ve(),Zo)),iCt=new Ps("externalPortSize",new Ca),Vlt=new Vi("externalPortReplacedDummies"),eG=new Vi("externalPortReplacedDummy"),By=new Ps("externalPortConnections",(t=u(Vf(Xa),9),new sh(t,u(ff(t,t.length),9),0))),Fv=new Ps(Xfe,0),tCt=new Vi("barycenterAssociates"),z6=new Vi("TopSideComments"),N6=new Vi("BottomSideComments"),ZV=new Vi("CommentConnectionPort"),Ult=new Ps("inputCollect",!1),Ylt=new Ps("outputCollect",!1),_O=new Ps("cyclic",!1),rCt=new Vi("crossHierarchyMap"),Qlt=new Vi("targetOffset"),new Ps("splineLabelSize",new Ca),Q4=new Vi("spacings"),nG=new Ps("partitionConstraint",!1),Iv=new Vi("breakingPoint.info"),hCt=new Vi("splines.survivingEdge"),R2=new Vi("splines.route.start"),Z4=new Vi("splines.edgeChain"),lCt=new Vi("originalPortConstraints"),x7=new Vi("selfLoopHolder"),k7=new Vi("splines.nsPortY"),Tc=new Vi("modelOrder"),Wlt=new Vi("longEdgeTargetNode"),Ov=new Ps(D1e,!1),X4=new Ps(D1e,!1),Glt=new Vi("layerConstraints.hiddenNodes"),uCt=new Vi("layerConstraints.opposidePort"),Xlt=new Vi("targetNode.modelOrder")}function Fxt(){Fxt=Z,kCt=(LD(),GV),gwe=new 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mn(z6t,CCt),_Ct=(pD(),Sht),ywe=new mn(q6t,_Ct),SCt=(cE(),PS),xwe=new mn(cH,SCt),Ewe=new mn(uH,.2),wwe=new mn(hct,2),fve=new mn(H6t,null),gve=new mn(V6t,10),dve=new mn(G6t,10),pve=new mn(U6t,20),pe(0),uve=new mn(W6t,pe(0)),pe(0),lve=new mn(Y6t,pe(0)),pe(0),hve=new mn(K6t,pe(0)),V2e=new mn(fct,!1),gCt=(kE(),mS),U2e=new mn(X6t,gCt),dCt=(H$(),Alt),G2e=new mn(Q6t,dCt),Lwe=new mn(lH,!1),pe(0),Awe=new mn(dct,pe(16)),pe(0),Mwe=new mn(gct,pe(5)),jCt=(Cz(),Mht),Bve=new mn(tg,jCt),vve=new mn(hH,10),xve=new mn(fH,1),RCt=(oz(),VV),Ave=new mn(V_,RCt),Tve=new Vi(pct),BCt=pe(1),pe(0),_ve=new mn(bct,BCt),$Ct=(vz(),Lht),zve=new mn(dH,$Ct),Rve=new Vi(gH),Ove=new mn(pH,!0),Dve=new mn(bH,2),Fve=new mn(wct,!0),TCt=(dq(),UV),bwe=new mn(Z6t,TCt),ECt=(h6(),p7),pwe=new mn(J6t,ECt),wCt=(V0(),vb),Z2e=new mn(wH,wCt),Q2e=new mn(tkt,!1),pCt=(iv(),q4),W2e=new mn(vct,pCt),bCt=(Z9(),vht),X2e=new mn(ekt,bCt),Y2e=new mn(mct,0),K2e=new mn(yct,0),Owe=Dlt,Iwe=EO,$we=mG,qwe=mG,Fwe=bht,owe=(G0(),sp),hwe=P6,swe=P6,nwe=P6,rwe=sp,Jwe=IS,tve=DS,Kwe=DS,Qwe=DS,nve=kht,ave=IS,sve=IS,kwe=(W0(),X6),Twe=X6,Cwe=PS,vwe=eP,mve=L7,yve=Yy,kve=L7,Eve=Yy,Lve=L7,Mve=Yy,Cve=Llt,Sve=VV,qve=L7,Hve=Yy,jve=L7,$ve=Yy,Pve=Yy,Ive=Yy,Nve=Yy}function ro(){ro=Z,J7t=new ms("DIRECTION_PREPROCESSOR",0),X7t=new ms("COMMENT_PREPROCESSOR",1),gS=new ms("EDGE_AND_LAYER_CONSTRAINT_EDGE_REVERSER",2),glt=new ms("INTERACTIVE_EXTERNAL_PORT_POSITIONER",3),vTt=new ms("PARTITION_PREPROCESSOR",4),CV=new ms("LABEL_DUMMY_INSERTER",5),FV=new ms("SELF_LOOP_PREPROCESSOR",6),h7=new ms("LAYER_CONSTRAINT_PREPROCESSOR",7),bTt=new ms("PARTITION_MIDPROCESSOR",8),oTt=new ms("HIGH_DEGREE_NODE_LAYER_PROCESSOR",9),gTt=new ms("NODE_PROMOTION",10),l7=new ms("LAYER_CONSTRAINT_POSTPROCESSOR",11),wTt=new ms("PARTITION_POSTPROCESSOR",12),iTt=new ms("HIERARCHICAL_PORT_CONSTRAINT_PROCESSOR",13),mTt=new ms("SEMI_INTERACTIVE_CROSSMIN_PROCESSOR",14),V7t=new ms("BREAKING_POINT_INSERTER",15),LV=new ms("LONG_EDGE_SPLITTER",16),plt=new ms("PORT_SIDE_PROCESSOR",17),EV=new ms("INVERTED_PORT_PROCESSOR",18),IV=new ms("PORT_LIST_SORTER",19),xTt=new ms("SORT_BY_INPUT_ORDER_OF_MODEL",20),DV=new ms("NORTH_SOUTH_PORT_PREPROCESSOR",21),G7t=new ms("BREAKING_POINT_PROCESSOR",22),pTt=new ms(E1e,23),kTt=new ms(T1e,24),OV=new ms("SELF_LOOP_PORT_RESTORER",25),yTt=new ms("SINGLE_EDGE_GRAPH_WRAPPER",26),TV=new ms("IN_LAYER_CONSTRAINT_PROCESSOR",27),eTt=new ms("END_NODE_PORT_LABEL_MANAGEMENT_PROCESSOR",28),fTt=new ms("LABEL_AND_NODE_SIZE_PROCESSOR",29),hTt=new ms("INNERMOST_NODE_MARGIN_CALCULATOR",30),NV=new ms("SELF_LOOP_ROUTER",31),Y7t=new ms("COMMENT_NODE_MARGIN_CALCULATOR",32),kV=new ms("END_LABEL_PREPROCESSOR",33),SV=new ms("LABEL_DUMMY_SWITCHER",34),W7t=new ms("CENTER_LABEL_MANAGEMENT_PROCESSOR",35),u7=new ms("LABEL_SIDE_SELECTOR",36),uTt=new ms("HYPEREDGE_DUMMY_MERGER",37),sTt=new ms("HIERARCHICAL_PORT_DUMMY_SIZE_PROCESSOR",38),dTt=new ms("LAYER_SIZE_AND_GRAPH_HEIGHT_CALCULATOR",39),pS=new ms("HIERARCHICAL_PORT_POSITION_PROCESSOR",40),Q7t=new ms("CONSTRAINTS_POSTPROCESSOR",41),K7t=new ms("COMMENT_POSTPROCESSOR",42),lTt=new ms("HYPERNODE_PROCESSOR",43),aTt=new ms("HIERARCHICAL_PORT_ORTHOGONAL_EDGE_ROUTER",44),AV=new ms("LONG_EDGE_JOINER",45),PV=new ms("SELF_LOOP_POSTPROCESSOR",46),U7t=new ms("BREAKING_POINT_REMOVER",47),MV=new ms("NORTH_SOUTH_PORT_POSTPROCESSOR",48),cTt=new ms("HORIZONTAL_COMPACTOR",49),_V=new ms("LABEL_DUMMY_REMOVER",50),nTt=new ms("FINAL_SPLINE_BENDPOINTS_CALCULATOR",51),tTt=new ms("END_LABEL_SORTER",52),xO=new ms("REVERSED_EDGE_RESTORER",53),xV=new ms("END_LABEL_POSTPROCESSOR",54),rTt=new ms("HIERARCHICAL_NODE_RESIZER",55),Z7t=new ms("DIRECTION_POSTPROCESSOR",56)}function zxn(t,e,n){var 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numbers.",WI="org.eclipse.elk.core.math",p1e={3:1,4:1,142:1,207:1,414:1},b1e={3:1,4:1,116:1,207:1,414:1},Gn="org.eclipse.elk.layered",Kg="org.eclipse.elk.alg.layered.graph.transform",w1e="ElkGraphImporter",v1e="ElkGraphImporter/lambda$0$Type",m1e="ElkGraphImporter/lambda$1$Type",y1e="ElkGraphImporter/lambda$2$Type",x1e="ElkGraphImporter/lambda$4$Type",k1e="Node margin calculation",$n="org.eclipse.elk.alg.layered.intermediate",E1e="ONE_SIDED_GREEDY_SWITCH",T1e="TWO_SIDED_GREEDY_SWITCH",Yot="No implementation is available for the layout processor ",T6t="IntermediateProcessorStrategy",Kot="Node '",C1e="FIRST_SEPARATE",_1e="LAST_SEPARATE",S1e="Odd port side processing",_s="org.eclipse.elk.alg.layered.intermediate.compaction",z_="org.eclipse.elk.alg.layered.intermediate.greedyswitch",c0="org.eclipse.elk.alg.layered.p3order.counting",YI={225:1},S6="org.eclipse.elk.alg.layered.intermediate.loops",Gl="org.eclipse.elk.alg.layered.intermediate.loops.ordering",cb="org.eclipse.elk.alg.layered.intermediate.loops.routing",q_="org.eclipse.elk.alg.layered.intermediate.preserveorder",Cd="org.eclipse.elk.alg.layered.intermediate.wrapping",kc="org.eclipse.elk.alg.layered.options",Xot="INTERACTIVE",A1e="DEPTH_FIRST",L1e="EDGE_LENGTH",M1e="SELF_LOOPS",D1e="firstTryWithInitialOrder",C6t="org.eclipse.elk.layered.directionCongruency",_6t="org.eclipse.elk.layered.feedbackEdges",sH="org.eclipse.elk.layered.interactiveReferencePoint",S6t="org.eclipse.elk.layered.mergeEdges",A6t="org.eclipse.elk.layered.mergeHierarchyEdges",L6t="org.eclipse.elk.layered.allowNonFlowPortsToSwitchSides",M6t="org.eclipse.elk.layered.portSortingStrategy",D6t="org.eclipse.elk.layered.thoroughness",I6t="org.eclipse.elk.layered.unnecessaryBendpoints",O6t="org.eclipse.elk.layered.generatePositionAndLayerIds",Qot="org.eclipse.elk.layered.cycleBreaking.strategy",KI="org.eclipse.elk.layered.layering.strategy",P6t="org.eclipse.elk.layered.layering.layerConstraint",F6t="org.eclipse.elk.layered.layering.layerChoiceConstraint",N6t="org.eclipse.elk.layered.layering.layerId",Zot="org.eclipse.elk.layered.layering.minWidth.upperBoundOnWidth",Jot="org.eclipse.elk.layered.layering.minWidth.upperLayerEstimationScalingFactor",tct="org.eclipse.elk.layered.layering.nodePromotion.strategy",ect="org.eclipse.elk.layered.layering.nodePromotion.maxIterations",nct="org.eclipse.elk.layered.layering.coffmanGraham.layerBound",H_="org.eclipse.elk.layered.crossingMinimization.strategy",B6t="org.eclipse.elk.layered.crossingMinimization.forceNodeModelOrder",rct="org.eclipse.elk.layered.crossingMinimization.hierarchicalSweepiness",ict="org.eclipse.elk.layered.crossingMinimization.semiInteractive",R6t="org.eclipse.elk.layered.crossingMinimization.positionChoiceConstraint",j6t="org.eclipse.elk.layered.crossingMinimization.positionId",$6t="org.eclipse.elk.layered.crossingMinimization.greedySwitch.activationThreshold",sct="org.eclipse.elk.layered.crossingMinimization.greedySwitch.type",aH="org.eclipse.elk.layered.crossingMinimization.greedySwitchHierarchical.type",I4="org.eclipse.elk.layered.nodePlacement.strategy",oH="org.eclipse.elk.layered.nodePlacement.favorStraightEdges",act="org.eclipse.elk.layered.nodePlacement.bk.edgeStraightening",oct="org.eclipse.elk.layered.nodePlacement.bk.fixedAlignment",cct="org.eclipse.elk.layered.nodePlacement.linearSegments.deflectionDampening",uct="org.eclipse.elk.layered.nodePlacement.networkSimplex.nodeFlexibility",lct="org.eclipse.elk.layered.nodePlacement.networkSimplex.nodeFlexibility.default",z6t="org.eclipse.elk.layered.edgeRouting.selfLoopDistribution",q6t="org.eclipse.elk.layered.edgeRouting.selfLoopOrdering",cH="org.eclipse.elk.layered.edgeRouting.splines.mode",uH="org.eclipse.elk.layered.edgeRouting.splines.sloppy.layerSpacingFactor",hct="org.eclipse.elk.layered.edgeRouting.polyline.slopedEdgeZoneWidth",H6t="org.eclipse.elk.layered.spacing.baseValue",V6t="org.eclipse.elk.layered.spacing.edgeNodeBetweenLayers",G6t="org.eclipse.elk.layered.spacing.edgeEdgeBetweenLayers",U6t="org.eclipse.elk.layered.spacing.nodeNodeBetweenLayers",W6t="org.eclipse.elk.layered.priority.direction",Y6t="org.eclipse.elk.layered.priority.shortness",K6t="org.eclipse.elk.layered.priority.straightness",fct="org.eclipse.elk.layered.compaction.connectedComponents",X6t="org.eclipse.elk.layered.compaction.postCompaction.strategy",Q6t="org.eclipse.elk.layered.compaction.postCompaction.constraints",lH="org.eclipse.elk.layered.highDegreeNodes.treatment",dct="org.eclipse.elk.layered.highDegreeNodes.threshold",gct="org.eclipse.elk.layered.highDegreeNodes.treeHeight",tg="org.eclipse.elk.layered.wrapping.strategy",hH="org.eclipse.elk.layered.wrapping.additionalEdgeSpacing",fH="org.eclipse.elk.layered.wrapping.correctionFactor",V_="org.eclipse.elk.layered.wrapping.cutting.strategy",pct="org.eclipse.elk.layered.wrapping.cutting.cuts",bct="org.eclipse.elk.layered.wrapping.cutting.msd.freedom",dH="org.eclipse.elk.layered.wrapping.validify.strategy",gH="org.eclipse.elk.layered.wrapping.validify.forbiddenIndices",pH="org.eclipse.elk.layered.wrapping.multiEdge.improveCuts",bH="org.eclipse.elk.layered.wrapping.multiEdge.distancePenalty",wct="org.eclipse.elk.layered.wrapping.multiEdge.improveWrappedEdges",Z6t="org.eclipse.elk.layered.edgeLabels.sideSelection",J6t="org.eclipse.elk.layered.edgeLabels.centerLabelPlacementStrategy",wH="org.eclipse.elk.layered.considerModelOrder.strategy",tkt="org.eclipse.elk.layered.considerModelOrder.noModelOrder",vct="org.eclipse.elk.layered.considerModelOrder.components",ekt="org.eclipse.elk.layered.considerModelOrder.longEdgeStrategy",mct="org.eclipse.elk.layered.considerModelOrder.crossingCounterNodeInfluence",yct="org.eclipse.elk.layered.considerModelOrder.crossingCounterPortInfluence",xct="layering",I1e="layering.minWidth",O1e="layering.nodePromotion",XI="crossingMinimization",vH="org.eclipse.elk.hierarchyHandling",P1e="crossingMinimization.greedySwitch",F1e="nodePlacement",N1e="nodePlacement.bk",B1e="edgeRouting",QI="org.eclipse.elk.edgeRouting",R1="spacing",nkt="priority",rkt="compaction",R1e="compaction.postCompaction",j1e="Specifies whether and how post-process compaction is applied.",ikt="highDegreeNodes",skt="wrapping",$1e="wrapping.cutting",z1e="wrapping.validify",akt="wrapping.multiEdge",kct="edgeLabels",ZI="considerModelOrder",okt="org.eclipse.elk.spacing.commentComment",ckt="org.eclipse.elk.spacing.commentNode",ukt="org.eclipse.elk.spacing.edgeEdge",lkt="org.eclipse.elk.spacing.edgeNode",hkt="org.eclipse.elk.spacing.labelLabel",fkt="org.eclipse.elk.spacing.labelPortHorizontal",dkt="org.eclipse.elk.spacing.labelPortVertical",gkt="org.eclipse.elk.spacing.labelNode",pkt="org.eclipse.elk.spacing.nodeSelfLoop",bkt="org.eclipse.elk.spacing.portPort",wkt="org.eclipse.elk.spacing.individual",vkt="org.eclipse.elk.port.borderOffset",mkt="org.eclipse.elk.noLayout",ykt="org.eclipse.elk.port.side",JI="org.eclipse.elk.debugMode",xkt="org.eclipse.elk.alignment",kkt="org.eclipse.elk.insideSelfLoops.activate",Ekt="org.eclipse.elk.insideSelfLoops.yo",Ect="org.eclipse.elk.nodeSize.fixedGraphSize",Tkt="org.eclipse.elk.direction",Ckt="org.eclipse.elk.nodeLabels.padding",_kt="org.eclipse.elk.portLabels.nextToPortIfPossible",Skt="org.eclipse.elk.portLabels.treatAsGroup",Akt="org.eclipse.elk.portAlignment.default",Lkt="org.eclipse.elk.portAlignment.north",Mkt="org.eclipse.elk.portAlignment.south",Dkt="org.eclipse.elk.portAlignment.west",Ikt="org.eclipse.elk.portAlignment.east",mH="org.eclipse.elk.contentAlignment",Okt="org.eclipse.elk.junctionPoints",Pkt="org.eclipse.elk.edgeLabels.placement",Fkt="org.eclipse.elk.port.index",Nkt="org.eclipse.elk.commentBox",Bkt="org.eclipse.elk.hypernode",Rkt="org.eclipse.elk.port.anchor",Tct="org.eclipse.elk.partitioning.activate",Cct="org.eclipse.elk.partitioning.partition",yH="org.eclipse.elk.position",jkt="org.eclipse.elk.margins",$kt="org.eclipse.elk.spacing.portsSurrounding",_ct="org.eclipse.elk.interactiveLayout",Ec="org.eclipse.elk.core.util",zkt={3:1,4:1,5:1,593:1},q1e="NETWORK_SIMPLEX",zc={123:1,51:1},xH="org.eclipse.elk.alg.layered.p1cycles",_y="org.eclipse.elk.alg.layered.p2layers",qkt={402:1,225:1},H1e={832:1,3:1,4:1},qu="org.eclipse.elk.alg.layered.p3order",uo="org.eclipse.elk.alg.layered.p4nodes",V1e={3:1,4:1,5:1,840:1},_d=1e-5,ub="org.eclipse.elk.alg.layered.p4nodes.bk",Sct="org.eclipse.elk.alg.layered.p5edges",t1="org.eclipse.elk.alg.layered.p5edges.orthogonal",Act="org.eclipse.elk.alg.layered.p5edges.orthogonal.direction",Lct=1e-6,Sy="org.eclipse.elk.alg.layered.p5edges.splines",Mct=.09999999999999998,kH=1e-8,G1e=4.71238898038469,U1e=3.141592653589793,G_="org.eclipse.elk.alg.mrtree",U_="org.eclipse.elk.alg.mrtree.graph",A6="org.eclipse.elk.alg.mrtree.intermediate",W1e="Set neighbors in level",Y1e="DESCENDANTS",Hkt="org.eclipse.elk.mrtree.weighting",Vkt="org.eclipse.elk.mrtree.searchOrder",EH="org.eclipse.elk.alg.mrtree.options",Xg="org.eclipse.elk.mrtree",K1e="org.eclipse.elk.tree",Gkt="org.eclipse.elk.alg.radial",O4=6.283185307179586,Ukt=5e-324,X1e="org.eclipse.elk.alg.radial.intermediate",Dct="org.eclipse.elk.alg.radial.intermediate.compaction",Q1e={3:1,4:1,5:1,106:1},Wkt="org.eclipse.elk.alg.radial.intermediate.optimization",Ict="No implementation is available for the layout option ",W_="org.eclipse.elk.alg.radial.options",Ykt="org.eclipse.elk.radial.orderId",Kkt="org.eclipse.elk.radial.radius",Oct="org.eclipse.elk.radial.compactor",Pct="org.eclipse.elk.radial.compactionStepSize",Xkt="org.eclipse.elk.radial.sorter",Qkt="org.eclipse.elk.radial.wedgeCriteria",Zkt="org.eclipse.elk.radial.optimizationCriteria",Sd="org.eclipse.elk.radial",Z1e="org.eclipse.elk.alg.radial.p1position.wedge",Jkt="org.eclipse.elk.alg.radial.sorting",J1e=5.497787143782138,tde=3.9269908169872414,ede=2.356194490192345,nde="org.eclipse.elk.alg.rectpacking",TH="org.eclipse.elk.alg.rectpacking.firstiteration",Fct="org.eclipse.elk.alg.rectpacking.options",t8t="org.eclipse.elk.rectpacking.optimizationGoal",e8t="org.eclipse.elk.rectpacking.lastPlaceShift",n8t="org.eclipse.elk.rectpacking.currentPosition",r8t="org.eclipse.elk.rectpacking.desiredPosition",i8t="org.eclipse.elk.rectpacking.onlyFirstIteration",s8t="org.eclipse.elk.rectpacking.rowCompaction",Nct="org.eclipse.elk.rectpacking.expandToAspectRatio",a8t="org.eclipse.elk.rectpacking.targetWidth",CH="org.eclipse.elk.expandNodes",Ph="org.eclipse.elk.rectpacking",tO="org.eclipse.elk.alg.rectpacking.util",_H="No implementation available for ",Ay="org.eclipse.elk.alg.spore",Ly="org.eclipse.elk.alg.spore.options",kv="org.eclipse.elk.sporeCompaction",Bct="org.eclipse.elk.underlyingLayoutAlgorithm",o8t="org.eclipse.elk.processingOrder.treeConstruction",c8t="org.eclipse.elk.processingOrder.spanningTreeCostFunction",Rct="org.eclipse.elk.processingOrder.preferredRoot",jct="org.eclipse.elk.processingOrder.rootSelection",$ct="org.eclipse.elk.structure.structureExtractionStrategy",u8t="org.eclipse.elk.compaction.compactionStrategy",l8t="org.eclipse.elk.compaction.orthogonal",h8t="org.eclipse.elk.overlapRemoval.maxIterations",f8t="org.eclipse.elk.overlapRemoval.runScanline",zct="processingOrder",rde="overlapRemoval",YE="org.eclipse.elk.sporeOverlap",ide="org.eclipse.elk.alg.spore.p1structure",qct="org.eclipse.elk.alg.spore.p2processingorder",Hct="org.eclipse.elk.alg.spore.p3execution",sde="Invalid index: ",KE="org.eclipse.elk.core.alg",P4={331:1},My={288:1},ade="Make sure its type is registered with the ",d8t=" utility class.",XE="true",Vct="false",ode="Couldn't clone property '",Ev=.05,Fh="org.eclipse.elk.core.options",cde=1.2999999523162842,Tv="org.eclipse.elk.box",g8t="org.eclipse.elk.box.packingMode",ude="org.eclipse.elk.algorithm",lde="org.eclipse.elk.resolvedAlgorithm",p8t="org.eclipse.elk.bendPoints",Uxn="org.eclipse.elk.labelManager",hde="org.eclipse.elk.scaleFactor",fde="org.eclipse.elk.animate",dde="org.eclipse.elk.animTimeFactor",gde="org.eclipse.elk.layoutAncestors",pde="org.eclipse.elk.maxAnimTime",bde="org.eclipse.elk.minAnimTime",wde="org.eclipse.elk.progressBar",vde="org.eclipse.elk.validateGraph",mde="org.eclipse.elk.validateOptions",yde="org.eclipse.elk.zoomToFit",Wxn="org.eclipse.elk.font.name",xde="org.eclipse.elk.font.size",kde="org.eclipse.elk.edge.type",Ede="partitioning",Tde="nodeLabels",SH="portAlignment",Gct="nodeSize",Uct="port",b8t="portLabels",Cde="insideSelfLoops",Y_="org.eclipse.elk.fixed",AH="org.eclipse.elk.random",_de="port must have a parent node to calculate the port side",Sde="The edge needs to have exactly one edge section. Found: ",K_="org.eclipse.elk.core.util.adapters",ph="org.eclipse.emf.ecore",F4="org.eclipse.elk.graph",Ade="EMapPropertyHolder",Lde="ElkBendPoint",Mde="ElkGraphElement",Dde="ElkConnectableShape",w8t="ElkEdge",Ide="ElkEdgeSection",Ode="EModelElement",Pde="ENamedElement",v8t="ElkLabel",m8t="ElkNode",y8t="ElkPort",Fde={92:1,90:1},L6="org.eclipse.emf.common.notify.impl",lb="The feature '",X_="' is not a valid changeable feature",Nde="Expecting null",Wct="' is not a valid feature",Bde="The feature ID",Rde=" is not a valid feature ID",dc=32768,jde={105:1,92:1,90:1,56:1,49:1,97:1},Mn="org.eclipse.emf.ecore.impl",M2="org.eclipse.elk.graph.impl",Q_="Recursive containment not allowed for ",QE="The datatype '",Cv="' is not a valid classifier",Yct="The value '",N4={190:1,3:1,4:1},Kct="The class '",ZE="http://www.eclipse.org/elk/ElkGraph",xf=1024,x8t="property",Z_="value",Xct="source",$de="properties",zde="identifier",Qct="height",Zct="width",Jct="parent",tut="text",eut="children",qde="hierarchical",k8t="sources",nut="targets",E8t="sections",LH="bendPoints",T8t="outgoingShape",C8t="incomingShape",_8t="outgoingSections",S8t="incomingSections",Ra="org.eclipse.emf.common.util",A8t="Severe implementation error in the Json to ElkGraph importer.",Ad="id",ma="org.eclipse.elk.graph.json",L8t="Unhandled parameter types: ",Hde="startPoint",Vde="An edge must have at least one source and one target (edge id: '",JE="').",Gde="Referenced edge section does not exist: ",Ude=" (edge id: '",M8t="target",Wde="sourcePoint",Yde="targetPoint",MH="group",ci="name",Kde="connectableShape cannot be null",Xde="edge cannot be null",rut="Passed edge is not 'simple'.",DH="org.eclipse.elk.graph.util",eO="The 'no duplicates' constraint is violated",iut="targetIndex=",D2=", size=",sut="sourceIndex=",Ld={3:1,4:1,20:1,28:1,52:1,14:1,15:1,54:1,67:1,63:1,58:1},aut={3:1,4:1,20:1,28:1,52:1,14:1,47:1,15:1,54:1,67:1,63:1,58:1,588:1},IH="logging",Qde="measureExecutionTime",Zde="parser.parse.1",Jde="parser.parse.2",OH="parser.next.1",out="parser.next.2",t0e="parser.next.3",e0e="parser.next.4",I2="parser.factor.1",D8t="parser.factor.2",n0e="parser.factor.3",r0e="parser.factor.4",i0e="parser.factor.5",s0e="parser.factor.6",a0e="parser.atom.1",o0e="parser.atom.2",c0e="parser.atom.3",I8t="parser.atom.4",cut="parser.atom.5",O8t="parser.cc.1",PH="parser.cc.2",u0e="parser.cc.3",l0e="parser.cc.5",P8t="parser.cc.6",F8t="parser.cc.7",uut="parser.cc.8",h0e="parser.ope.1",f0e="parser.ope.2",d0e="parser.ope.3",Qg="parser.descape.1",g0e="parser.descape.2",p0e="parser.descape.3",b0e="parser.descape.4",w0e="parser.descape.5",bh="parser.process.1",v0e="parser.quantifier.1",m0e="parser.quantifier.2",y0e="parser.quantifier.3",x0e="parser.quantifier.4",N8t="parser.quantifier.5",k0e="org.eclipse.emf.common.notify",B8t={415:1,672:1},E0e={3:1,4:1,20:1,28:1,52:1,14:1,15:1,67:1,58:1},nO={366:1,143:1},J_="index=",lut={3:1,4:1,5:1,126:1},T0e={3:1,4:1,20:1,28:1,52:1,14:1,15:1,54:1,67:1,58:1},R8t={3:1,6:1,4:1,5:1,192:1},C0e={3:1,4:1,5:1,165:1,367:1},_0e=";/?:@&=+$,",S0e="invalid authority: ",A0e="EAnnotation",L0e="ETypedElement",M0e="EStructuralFeature",D0e="EAttribute",I0e="EClassifier",O0e="EEnumLiteral",P0e="EGenericType",F0e="EOperation",N0e="EParameter",B0e="EReference",R0e="ETypeParameter",$i="org.eclipse.emf.ecore.util",hut={76:1},j8t={3:1,20:1,14:1,15:1,58:1,589:1,76:1,69:1,95:1},j0e="org.eclipse.emf.ecore.util.FeatureMap$Entry",Hu=8192,Dy=2048,tS="byte",FH="char",eS="double",nS="float",rS="int",iS="long",sS="short",$0e="java.lang.Object",B4={3:1,4:1,5:1,247:1},$8t={3:1,4:1,5:1,673:1},z0e={3:1,4:1,20:1,28:1,52:1,14:1,15:1,54:1,67:1,63:1,58:1,69:1},zo={3:1,4:1,20:1,28:1,52:1,14:1,15:1,54:1,67:1,63:1,58:1,76:1,69:1,95:1},rO="mixed",Yr="http:///org/eclipse/emf/ecore/util/ExtendedMetaData",Nh="kind",q0e={3:1,4:1,5:1,674:1},z8t={3:1,4:1,20:1,28:1,52:1,14:1,15:1,67:1,58:1,76:1,69:1,95:1},NH={20:1,28:1,52:1,14:1,15:1,58:1,69:1},BH={47:1,125:1,279:1},RH={72:1,332:1},jH="The value of type '",$H="' must be of type 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For an orthogonal style it is set to true, for all other styles to false."),La),Rs),un(qn)))),ca(e,oH,I4,Jwe),ca(e,oH,I4,tve),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,act),N1e),"BK Edge Straightening"),"Specifies whether the Brandes Koepf node placer tries to increase the number of straight edges at the expense of diagram size. There is a subtle difference to the 'favorStraightEdges' option, which decides whether a balanced placement of the nodes is desired, or not. In bk terms this means combining the four alignments into a single balanced one, or not. This option on the other hand tries to straighten additional edges during the creation of each of the four alignments."),ICt),us),$Tt),un(qn)))),ca(e,act,I4,Kwe),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,oct),N1e),"BK Fixed Alignment"),"Tells the BK node placer to use a certain alignment (out of its four) instead of the one producing the smallest height, or the combination of all four."),OCt),us),GTt),un(qn)))),ca(e,oct,I4,Qwe),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,cct),"nodePlacement.linearSegments"),"Linear Segments Deflection Dampening"),"Dampens the movement of nodes to keep the diagram from getting too large."),.3),Oo),la),un(qn)))),ca(e,cct,I4,nve),an(e,new Xe(rn(nn(sn(Ze(en(Je(tn(new Ue,uct),"nodePlacement.networkSimplex"),"Node Flexibility"),"Aims at shorter and straighter edges. Two configurations are possible: (a) allow ports to move freely on the side they are assigned to (the order is always defined beforehand), (b) additionally allow to enlarge a node wherever it helps. If this option is not configured for a node, the 'nodeFlexibility.default' value is used, which is specified for the node's parent."),us),yht),un(ea)))),ca(e,uct,I4,ave),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,lct),"nodePlacement.networkSimplex.nodeFlexibility"),"Node Flexibility Default"),"Default value of the 'nodeFlexibility' option for the children of a hierarchical node."),PCt),us),yht),un(qn)))),ca(e,lct,I4,sve),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,z6t),B1e),"Self-Loop Distribution"),"Alter the distribution of the loops around the node. It only takes effect for PortConstraints.FREE."),CCt),us),W9t),un(ea)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,q6t),B1e),"Self-Loop Ordering"),"Alter the ordering of the loops they can either be stacked or sequenced. It only takes effect for PortConstraints.FREE."),_Ct),us),Y9t),un(ea)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,cH),"edgeRouting.splines"),"Spline Routing Mode"),"Specifies the way control points are assembled for each individual edge. CONSERVATIVE ensures that edges are properly routed around the nodes but feels rather orthogonal at times. SLOPPY uses fewer control points to obtain curvier edge routes but may result in edges overlapping nodes."),SCt),us),X9t),un(qn)))),ca(e,cH,QI,kwe),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,uH),"edgeRouting.splines.sloppy"),"Sloppy Spline Layer Spacing Factor"),"Spacing factor for routing area between layers when using sloppy spline routing."),.2),Oo),la),un(qn)))),ca(e,uH,QI,Twe),ca(e,uH,cH,Cwe),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,hct),"edgeRouting.polyline"),"Sloped Edge Zone Width"),"Width of the strip to the left and to the right of each layer where the polyline edge router is allowed to refrain from ensuring that edges are routed horizontally. This prevents awkward bend points for nodes that extent almost to the edge of their layer."),2),Oo),la),un(qn)))),ca(e,hct,QI,vwe),an(e,new Xe(rn(nn(sn(Ze(en(Je(tn(new Ue,H6t),R1),"Spacing Base Value"),"An optional base value for all other layout options of the 'spacing' group. It can be used to conveniently alter the overall 'spaciousness' of the drawing. Whenever an explicit value is set for the other layout options, this base value will have no effect. The base value is not inherited, i.e. it must be set for each hierarchical node."),Oo),la),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,V6t),R1),"Edge Node Between Layers Spacing"),"The spacing to be preserved between nodes and edges that are routed next to the node's layer. For the spacing between nodes and edges that cross the node's layer 'spacing.edgeNode' is used."),10),Oo),la),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,G6t),R1),"Edge Edge Between Layer Spacing"),"Spacing to be preserved between pairs of edges that are routed between the same pair of layers. Note that 'spacing.edgeEdge' is used for the spacing between pairs of edges crossing the same layer."),10),Oo),la),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,U6t),R1),"Node Node Between Layers Spacing"),"The spacing to be preserved between any pair of nodes of two adjacent layers. Note that 'spacing.nodeNode' is used for the spacing between nodes within the layer itself."),20),Oo),la),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,W6t),nkt),"Direction Priority"),"Defines how important it is to have a certain edge point into the direction of the overall layout. This option is evaluated during the cycle breaking phase."),pe(0)),gc),ja),un(Pd)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,Y6t),nkt),"Shortness Priority"),"Defines how important it is to keep an edge as short as possible. This option is evaluated during the layering phase."),pe(0)),gc),ja),un(Pd)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,K6t),nkt),"Straightness Priority"),"Defines how important it is to keep an edge straight, i.e. aligned with one of the two axes. This option is evaluated during node placement."),pe(0)),gc),ja),un(Pd)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,fct),rkt),Jfe),"Tries to further compact components (disconnected sub-graphs)."),!1),La),Rs),un(qn)))),ca(e,fct,R_,!0),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,X6t),R1e),"Post Compaction Strategy"),j1e),gCt),us),QTt),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,Q6t),R1e),"Post Compaction Constraint Calculation"),j1e),dCt),us),LTt),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,lH),ikt),"High Degree Node Treatment"),"Makes room around high degree nodes to place leafs and trees."),!1),La),Rs),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,dct),ikt),"High Degree Node Threshold"),"Whether a node is considered to have a high degree."),pe(16)),gc),ja),un(qn)))),ca(e,dct,lH,!0),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,gct),ikt),"High Degree Node Maximum Tree Height"),"Maximum height of a subtree connected to a high degree node to be moved to separate layers."),pe(5)),gc),ja),un(qn)))),ca(e,gct,lH,!0),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,tg),skt),"Graph Wrapping Strategy"),"For certain graphs and certain prescribed drawing areas it may be desirable to split the laid out graph into chunks that are placed side by side. The edges that connect different chunks are 'wrapped' around from the end of one chunk to the start of the other chunk. The points between the chunks are referred to as 'cuts'."),jCt),us),t_t),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,hH),skt),"Additional Wrapped Edges Spacing"),"To visually separate edges that are wrapped from regularly routed edges an additional spacing value can be specified in form of this layout option. The spacing is added to the regular edgeNode spacing."),10),Oo),la),un(qn)))),ca(e,hH,tg,mve),ca(e,hH,tg,yve),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,fH),skt),"Correction Factor for Wrapping"),"At times and for certain types of graphs the executed wrapping may produce results that are consistently biased in the same fashion: either wrapping to often or to rarely. This factor can be used to correct the bias. Internally, it is simply multiplied with the 'aspect ratio' layout option."),1),Oo),la),un(qn)))),ca(e,fH,tg,kve),ca(e,fH,tg,Eve),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,V_),$1e),"Cutting Strategy"),"The strategy by which the layer indexes are determined at which the layering crumbles into chunks."),RCt),us),OTt),un(qn)))),ca(e,V_,tg,Lve),ca(e,V_,tg,Mve),an(e,new Xe(rn(nn(sn(Ze(en(Je(tn(new Ue,pct),$1e),"Manually Specified Cuts"),"Allows the user to specify her own cuts for a certain graph."),V1),wh),un(qn)))),ca(e,pct,V_,Cve),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,bct),"wrapping.cutting.msd"),"MSD Freedom"),"The MSD cutting strategy starts with an initial guess on the number of chunks the graph should be split into. The freedom specifies how much the strategy may deviate from this guess. E.g. if an initial number of 3 is computed, a freedom of 1 allows 2, 3, and 4 cuts."),BCt),gc),ja),un(qn)))),ca(e,bct,V_,Sve),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,dH),z1e),"Validification Strategy"),"When wrapping graphs, one can specify indices that are not allowed as split points. The validification strategy makes sure every computed split point is allowed."),$Ct),us),J9t),un(qn)))),ca(e,dH,tg,qve),ca(e,dH,tg,Hve),an(e,new Xe(rn(nn(sn(Ze(en(Je(tn(new Ue,gH),z1e),"Valid Indices for Wrapping"),null),V1),wh),un(qn)))),ca(e,gH,tg,jve),ca(e,gH,tg,$ve),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,pH),akt),"Improve Cuts"),"For general graphs it is important that not too many edges wrap backwards. Thus a compromise between evenly-distributed cuts and the total number of cut edges is sought."),!0),La),Rs),un(qn)))),ca(e,pH,tg,Pve),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,bH),akt),"Distance Penalty When Improving Cuts"),null),2),Oo),la),un(qn)))),ca(e,bH,tg,Ive),ca(e,bH,pH,!0),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,wct),akt),"Improve Wrapped Edges"),"The initial wrapping is performed in a very simple way. As a consequence, edges that wrap from one chunk to another may be unnecessarily long. Activating this option tries to shorten such edges."),!0),La),Rs),un(qn)))),ca(e,wct,tg,Nve),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,Z6t),kct),"Edge Label Side Selection"),"Method to decide on edge label sides."),TCt),us),RTt),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,J6t),kct),"Edge Center Label Placement Strategy"),"Determines in which layer center labels of long edges should be placed."),ECt),us),b7),ji(qn,lt(ct(ip,1),oe,175,0,[rp]))))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,wH),ZI),"Consider Model Order"),"Preserves the order of nodes and edges in the model file if this does not lead to additional edge crossings. Depending on the strategy this is not always possible since the node and edge order might be conflicting."),wCt),us),H9t),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,tkt),ZI),"No Model Order"),"Set on a node to not set a model order for this node even though it is a real node."),!1),La),Rs),un(ea)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,vct),ZI),"Consider Model Order for Components"),"If set to NONE the usual ordering strategy (by cumulative node priority and size of nodes) is used. INSIDE_PORT_SIDES orders the components with external ports only inside the groups with the same port side. FORCE_MODEL_ORDER enforces the mode order on components. This option might produce bad alignments and sub optimal drawings in terms of used area since the ordering should be respected."),pCt),us),F7t),un(qn)))),ca(e,vct,R_,null),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,ekt),ZI),"Long Edge Ordering Strategy"),"Indicates whether long edges are sorted under, over, or equal to nodes that have no connection to a previous layer in a left-to-right or right-to-left layout. Under and over changes to right and left in a vertical layout."),bCt),us),P9t),un(qn)))),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,mct),ZI),"Crossing Counter Node Order Influence"),"Indicates with what percentage (1 for 100%) violations of the node model order are weighted against the crossings e.g. a value of 0.5 means two model order violations are as important as on edge crossing. This allows some edge crossings in favor of preserving the model order. It is advised to set this value to a very small positive value (e.g. 0.001) to have minimal crossing and a optimal node order. Defaults to no influence (0)."),0),Oo),la),un(qn)))),ca(e,mct,wH,null),an(e,new Xe(rn(nn(sn(kn(Ze(en(Je(tn(new Ue,yct),ZI),"Crossing Counter Port Order Influence"),"Indicates with what percentage (1 for 100%) violations of the port model order are weighted against the crossings e.g. a value of 0.5 means two model order violations are as important as on edge crossing. This allows some edge crossings in favor of preserving the model order. It is advised to set this value to a very small positive value (e.g. 0.001) to have minimal crossing and a optimal port order. 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ss(this,0)),u(u(Bc(this.c,(Ii(),X2)),153),215)).kl();case 2:return r?(!this.b&&(this.b=new ss(this,2)),this.b):(!this.b&&(this.b=new ss(this,2)),this.b.b);case 3:return!this.c&&(this.c=new ss(this,0)),Br(SI(this.c,(Ii(),lA),!0));case 4:return gwt(this.a,(!this.c&&(this.c=new ss(this,0)),Br(SI(this.c,(Ii(),lA),!0))));case 5:return this.a}return uh(this,e-Jn((Ii(),f5)),yn(this.j&2?(!this.k&&(this.k=new nh),this.k).ck():f5,e),n,r)},l.lh=function(e){switch(e){case 0:return!!this.c&&this.c.i!=0;case 1:return!(!this.c&&(this.c=new ss(this,0)),u(Bc(this.c,(Ii(),X2)),153)).dc();case 2:return!!this.b&&this.b.i!=0;case 3:return!this.c&&(this.c=new ss(this,0)),Br(SI(this.c,(Ii(),lA),!0))!=null;case 4:return gwt(this.a,(!this.c&&(this.c=new ss(this,0)),Br(SI(this.c,(Ii(),lA),!0))))!=null;case 5:return!!this.a}return oh(this,e-Jn((Ii(),f5)),yn(this.j&2?(!this.k&&(this.k=new nh),this.k).ck():f5,e))},l.sh=function(e,n){switch(e){case 0:!this.c&&(this.c=new ss(this,0)),nD(this.c,n);return;case 1:(!this.c&&(this.c=new ss(this,0)),u(u(Bc(this.c,(Ii(),X2)),153),215)).Wb(n);return;case 2:!this.b&&(this.b=new ss(this,2)),nD(this.b,n);return;case 3:Jvt(this,Br(n));return;case 4:Jvt(this,pwt(this.a,n));return;case 5:vc(this,u(n,148));return}gh(this,e-Jn((Ii(),f5)),yn(this.j&2?(!this.k&&(this.k=new nh),this.k).ck():f5,e),n)},l.zh=function(){return Ii(),f5},l.Bh=function(e){switch(e){case 0:!this.c&&(this.c=new ss(this,0)),xr(this.c);return;case 1:(!this.c&&(this.c=new ss(this,0)),u(Bc(this.c,(Ii(),X2)),153)).$b();return;case 2:!this.b&&(this.b=new ss(this,2)),xr(this.b);return;case 3:!this.c&&(this.c=new ss(this,0)),Oq(this.c,(Ii(),lA),null);return;case 4:Jvt(this,pwt(this.a,null));return;case 5:this.a=null;return}fh(this,e-Jn((Ii(),f5)),yn(this.j&2?(!this.k&&(this.k=new nh),this.k).ck():f5,e))},F(xs,"SimpleAnyTypeImpl",668),D(669,506,{105:1,92:1,90:1,56:1,49:1,97:1,2023:1,669:1},qqt),l._g=function(e,n,r){switch(e){case 0:return r?(!this.a&&(this.a=new ss(this,0)),this.a):(!this.a&&(this.a=new ss(this,0)),this.a.b);case 1:return r?(!this.b&&(this.b=new _l((dn(),Qa),cc,this,1)),this.b):(!this.b&&(this.b=new _l((dn(),Qa),cc,this,1)),wD(this.b));case 2:return r?(!this.c&&(this.c=new _l((dn(),Qa),cc,this,2)),this.c):(!this.c&&(this.c=new _l((dn(),Qa),cc,this,2)),wD(this.c));case 3:return!this.a&&(this.a=new ss(this,0)),Bc(this.a,(Ii(),mP));case 4:return!this.a&&(this.a=new ss(this,0)),Bc(this.a,(Ii(),yP));case 5:return!this.a&&(this.a=new ss(this,0)),Bc(this.a,(Ii(),hA));case 6:return!this.a&&(this.a=new ss(this,0)),Bc(this.a,(Ii(),fA))}return uh(this,e-Jn((Ii(),Wv)),yn(this.j&2?(!this.k&&(this.k=new nh),this.k).ck():Wv,e),n,r)},l.jh=function(e,n,r){var s;switch(n){case 0:return!this.a&&(this.a=new ss(this,0)),EI(this.a,e,r);case 1:return!this.b&&(this.b=new _l((dn(),Qa),cc,this,1)),Oj(this.b,e,r);case 2:return!this.c&&(this.c=new _l((dn(),Qa),cc,this,2)),Oj(this.c,e,r);case 5:return!this.a&&(this.a=new ss(this,0)),WWt(Bc(this.a,(Ii(),hA)),e,r)}return s=u(yn(this.j&2?(!this.k&&(this.k=new nh),this.k).ck():(Ii(),Wv),n),66),s.Nj().Rj(this,$mt(this),n-Jn((Ii(),Wv)),e,r)},l.lh=function(e){switch(e){case 0:return!!this.a&&this.a.i!=0;case 1:return!!this.b&&this.b.f!=0;case 2:return!!this.c&&this.c.f!=0;case 3:return!this.a&&(this.a=new ss(this,0)),!hj(Bc(this.a,(Ii(),mP)));case 4:return!this.a&&(this.a=new ss(this,0)),!hj(Bc(this.a,(Ii(),yP)));case 5:return!this.a&&(this.a=new ss(this,0)),!hj(Bc(this.a,(Ii(),hA)));case 6:return!this.a&&(this.a=new ss(this,0)),!hj(Bc(this.a,(Ii(),fA)))}return oh(this,e-Jn((Ii(),Wv)),yn(this.j&2?(!this.k&&(this.k=new nh),this.k).ck():Wv,e))},l.sh=function(e,n){switch(e){case 0:!this.a&&(this.a=new ss(this,0)),nD(this.a,n);return;case 1:!this.b&&(this.b=new _l((dn(),Qa),cc,this,1)),xz(this.b,n);return;case 2:!this.c&&(this.c=new _l((dn(),Qa),cc,this,2)),xz(this.c,n);return;case 3:!this.a&&(this.a=new ss(this,0)),Tx(Bc(this.a,(Ii(),mP))),!this.a&&(this.a=new ss(this,0)),g9(Bc(this.a,mP),u(n,14));return;case 4:!this.a&&(this.a=new ss(this,0)),Tx(Bc(this.a,(Ii(),yP))),!this.a&&(this.a=new ss(this,0)),g9(Bc(this.a,yP),u(n,14));return;case 5:!this.a&&(this.a=new ss(this,0)),Tx(Bc(this.a,(Ii(),hA))),!this.a&&(this.a=new ss(this,0)),g9(Bc(this.a,hA),u(n,14));return;case 6:!this.a&&(this.a=new ss(this,0)),Tx(Bc(this.a,(Ii(),fA))),!this.a&&(this.a=new ss(this,0)),g9(Bc(this.a,fA),u(n,14));return}gh(this,e-Jn((Ii(),Wv)),yn(this.j&2?(!this.k&&(this.k=new nh),this.k).ck():Wv,e),n)},l.zh=function(){return Ii(),Wv},l.Bh=function(e){switch(e){case 0:!this.a&&(this.a=new ss(this,0)),xr(this.a);return;case 1:!this.b&&(this.b=new _l((dn(),Qa),cc,this,1)),this.b.c.$b();return;case 2:!this.c&&(this.c=new _l((dn(),Qa),cc,this,2)),this.c.c.$b();return;case 3:!this.a&&(this.a=new ss(this,0)),Tx(Bc(this.a,(Ii(),mP)));return;case 4:!this.a&&(this.a=new ss(this,0)),Tx(Bc(this.a,(Ii(),yP)));return;case 5:!this.a&&(this.a=new ss(this,0)),Tx(Bc(this.a,(Ii(),hA)));return;case 6:!this.a&&(this.a=new ss(this,0)),Tx(Bc(this.a,(Ii(),fA)));return}fh(this,e-Jn((Ii(),Wv)),yn(this.j&2?(!this.k&&(this.k=new nh),this.k).ck():Wv,e))},l.Ib=function(){var e;return this.j&4?mf(this):(e=new _h(mf(this)),e.a+=" (mixed: ",l9(e,this.a),e.a+=")",e.a)},F(xs,"XMLTypeDocumentRootImpl",669),D(1919,704,{105:1,92:1,90:1,471:1,147:1,56:1,108:1,49:1,97:1,150:1,114:1,115:1,2024:1},_m),l.Ih=function(e,n){switch(e.yj()){case 7:case 8:case 9:case 10:case 16:case 22:case 23:case 24:case 25:case 26:case 32:case 33:case 34:case 36:case 37:case 44:case 45:case 50:case 51:case 53:case 55:case 56:case 57:case 58:case 60:case 61:case 4:return n==null?null:$o(n);case 19:case 28:case 29:case 35:case 38:case 39:case 41:case 46:case 52:case 54:case 5:return Br(n);case 6:return bZe(u(n,190));case 12:case 47:case 49:case 11:return bhe(this,e,n);case 13:return n==null?null:r3n(u(n,240));case 15:case 14:return n==null?null:dnn(Xt(ye(n)));case 17:return mae((Ii(),n));case 18:return mae(n);case 21:case 20:return n==null?null:gnn(u(n,155).a);case 27:return wZe(u(n,190));case 30:return Fse((Ii(),u(n,15)));case 31:return Fse(u(n,15));case 40:return mZe((Ii(),n));case 42:return yae((Ii(),n));case 43:return yae(n);case 59:case 48:return vZe((Ii(),n));default:throw it(new Fn(QE+e.ne()+Cv))}},l.Jh=function(e){var n,r,s,o,h;switch(e.G==-1&&(e.G=(r=Rl(e),r?Hg(r.Mh(),e):-1)),e.G){case 0:return n=new Wpt,n;case 1:return s=new AB,s;case 2:return o=new Hqt,o;case 3:return h=new qqt,h;default:throw it(new Fn(Kct+e.zb+Cv))}},l.Kh=function(e,n){var r,s,o,h,d,v,k,C,M,j,H,G,K,tt,gt,Mt;switch(e.yj()){case 5:case 52:case 4:return n;case 6:return Ofn(n);case 8:case 7:return n==null?null:y0n(n);case 9:return n==null?null:AD(ql((s=$c(n,!0),s.length>0&&(Rr(0,s.length),s.charCodeAt(0)==43)?s.substr(1):s),-128,127)<<24>>24);case 10:return n==null?null:AD(ql((o=$c(n,!0),o.length>0&&(Rr(0,o.length),o.charCodeAt(0)==43)?o.substr(1):o),-128,127)<<24>>24);case 11:return Br(vv(this,(Ii(),I5e),n));case 12:return Br(vv(this,(Ii(),O5e),n));case 13:return n==null?null:new gbt($c(n,!0));case 15:case 14:return z2n(n);case 16:return Br(vv(this,(Ii(),P5e),n));case 17:return zie((Ii(),n));case 18:return zie(n);case 28:case 29:case 35:case 38:case 39:case 41:case 54:case 19:return $c(n,!0);case 21:case 20:return X2n(n);case 22:return Br(vv(this,(Ii(),F5e),n));case 23:return Br(vv(this,(Ii(),N5e),n));case 24:return Br(vv(this,(Ii(),B5e),n));case 25:return Br(vv(this,(Ii(),R5e),n));case 26:return Br(vv(this,(Ii(),j5e),n));case 27:return Afn(n);case 30:return qie((Ii(),n));case 31:return qie(n);case 32:return n==null?null:pe(ql((M=$c(n,!0),M.length>0&&(Rr(0,M.length),M.charCodeAt(0)==43)?M.substr(1):M),Sa,wi));case 33:return n==null?null:new Rp((j=$c(n,!0),j.length>0&&(Rr(0,j.length),j.charCodeAt(0)==43)?j.substr(1):j));case 34:return n==null?null:pe(ql((H=$c(n,!0),H.length>0&&(Rr(0,H.length),H.charCodeAt(0)==43)?H.substr(1):H),Sa,wi));case 36:return n==null?null:v2(Rq((G=$c(n,!0),G.length>0&&(Rr(0,G.length),G.charCodeAt(0)==43)?G.substr(1):G)));case 37:return n==null?null:v2(Rq((K=$c(n,!0),K.length>0&&(Rr(0,K.length),K.charCodeAt(0)==43)?K.substr(1):K)));case 40:return Vhn((Ii(),n));case 42:return Hie((Ii(),n));case 43:return Hie(n);case 44:return n==null?null:new Rp((tt=$c(n,!0),tt.length>0&&(Rr(0,tt.length),tt.charCodeAt(0)==43)?tt.substr(1):tt));case 45:return n==null?null:new Rp((gt=$c(n,!0),gt.length>0&&(Rr(0,gt.length),gt.charCodeAt(0)==43)?gt.substr(1):gt));case 46:return $c(n,!1);case 47:return Br(vv(this,(Ii(),$5e),n));case 59:case 48:return Hhn((Ii(),n));case 49:return Br(vv(this,(Ii(),z5e),n));case 50:return n==null?null:uE(ql((Mt=$c(n,!0),Mt.length>0&&(Rr(0,Mt.length),Mt.charCodeAt(0)==43)?Mt.substr(1):Mt),zH,32767)<<16>>16);case 51:return n==null?null:uE(ql((h=$c(n,!0),h.length>0&&(Rr(0,h.length),h.charCodeAt(0)==43)?h.substr(1):h),zH,32767)<<16>>16);case 53:return Br(vv(this,(Ii(),q5e),n));case 55:return n==null?null:uE(ql((d=$c(n,!0),d.length>0&&(Rr(0,d.length),d.charCodeAt(0)==43)?d.substr(1):d),zH,32767)<<16>>16);case 56:return n==null?null:uE(ql((v=$c(n,!0),v.length>0&&(Rr(0,v.length),v.charCodeAt(0)==43)?v.substr(1):v),zH,32767)<<16>>16);case 57:return n==null?null:v2(Rq((k=$c(n,!0),k.length>0&&(Rr(0,k.length),k.charCodeAt(0)==43)?k.substr(1):k)));case 58:return n==null?null:v2(Rq((C=$c(n,!0),C.length>0&&(Rr(0,C.length),C.charCodeAt(0)==43)?C.substr(1):C)));case 60:return n==null?null:pe(ql((r=$c(n,!0),r.length>0&&(Rr(0,r.length),r.charCodeAt(0)==43)?r.substr(1):r),Sa,wi));case 61:return n==null?null:pe(ql($c(n,!0),Sa,wi));default:throw it(new Fn(QE+e.ne()+Cv))}};var V5e,TLt,G5e,CLt;F(xs,"XMLTypeFactoryImpl",1919),D(586,179,{105:1,92:1,90:1,147:1,191:1,56:1,235:1,108:1,49:1,97:1,150:1,179:1,114:1,115:1,675:1,1945:1,586:1},AXt),l.N=!1,l.O=!1;var U5e=!1;F(xs,"XMLTypePackageImpl",586),D(1852,1,{837:1},hx),l._j=function(){return oxt(),exe},F(xs,"XMLTypePackageImpl/1",1852),D(1861,1,si,d1),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/10",1861),D(1862,1,si,LB),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/11",1862),D(1863,1,si,MB),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/12",1863),D(1864,1,si,DB),l.wj=function(e){return Bm(e)},l.xj=function(e){return Nt(la,ee,333,e,7,1)},F(xs,"XMLTypePackageImpl/13",1864),D(1865,1,si,IB),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/14",1865),D(1866,1,si,OB),l.wj=function(e){return _t(e,15)},l.xj=function(e){return Nt(wh,Ty,15,e,0,1)},F(xs,"XMLTypePackageImpl/15",1866),D(1867,1,si,PB),l.wj=function(e){return _t(e,15)},l.xj=function(e){return Nt(wh,Ty,15,e,0,1)},F(xs,"XMLTypePackageImpl/16",1867),D(1868,1,si,$f),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/17",1868),D(1869,1,si,du),l.wj=function(e){return _t(e,155)},l.xj=function(e){return Nt(i7,ee,155,e,0,1)},F(xs,"XMLTypePackageImpl/18",1869),D(1870,1,si,AJ),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/19",1870),D(1853,1,si,LJ),l.wj=function(e){return _t(e,843)},l.xj=function(e){return Nt(wP,De,843,e,0,1)},F(xs,"XMLTypePackageImpl/2",1853),D(1871,1,si,MJ),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/20",1871),D(1872,1,si,gu),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/21",1872),D(1873,1,si,cC),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/22",1873),D(1874,1,si,FB),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/23",1874),D(1875,1,si,NB),l.wj=function(e){return _t(e,190)},l.xj=function(e){return Nt(Gu,ee,190,e,0,2)},F(xs,"XMLTypePackageImpl/24",1875),D(1876,1,si,fx),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/25",1876),D(1877,1,si,DJ),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/26",1877),D(1878,1,si,$k),l.wj=function(e){return _t(e,15)},l.xj=function(e){return Nt(wh,Ty,15,e,0,1)},F(xs,"XMLTypePackageImpl/27",1878),D(1879,1,si,IJ),l.wj=function(e){return _t(e,15)},l.xj=function(e){return Nt(wh,Ty,15,e,0,1)},F(xs,"XMLTypePackageImpl/28",1879),D(1880,1,si,BB),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/29",1880),D(1854,1,si,OJ),l.wj=function(e){return _t(e,667)},l.xj=function(e){return Nt(mU,De,2021,e,0,1)},F(xs,"XMLTypePackageImpl/3",1854),D(1881,1,si,PJ),l.wj=function(e){return _t(e,19)},l.xj=function(e){return Nt(ja,ee,19,e,0,1)},F(xs,"XMLTypePackageImpl/30",1881),D(1882,1,si,uC),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/31",1882),D(1883,1,si,RB),l.wj=function(e){return _t(e,162)},l.xj=function(e){return Nt(Sv,ee,162,e,0,1)},F(xs,"XMLTypePackageImpl/32",1883),D(1884,1,si,UL),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/33",1884),D(1885,1,si,lC),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/34",1885),D(1886,1,si,FJ),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/35",1886),D(1887,1,si,NJ),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/36",1887),D(1888,1,si,WL),l.wj=function(e){return _t(e,15)},l.xj=function(e){return Nt(wh,Ty,15,e,0,1)},F(xs,"XMLTypePackageImpl/37",1888),D(1889,1,si,hC),l.wj=function(e){return 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Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/44",1895),D(1896,1,si,KL),l.wj=function(e){return _t(e,184)},l.xj=function(e){return Nt(Av,ee,184,e,0,1)},F(xs,"XMLTypePackageImpl/45",1896),D(1897,1,si,zf),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/46",1897),D(1898,1,si,dC),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/47",1898),D(1899,1,si,p1),l.wj=function(e){return ra(e)},l.xj=function(e){return Nt(Ae,ee,2,e,6,1)},F(xs,"XMLTypePackageImpl/48",1899),D(ab,1,si,b1),l.wj=function(e){return _t(e,184)},l.xj=function(e){return Nt(Av,ee,184,e,0,1)},F(xs,"XMLTypePackageImpl/49",ab),D(1856,1,si,RJ),l.wj=function(e){return _t(e,669)},l.xj=function(e){return Nt(kLt,De,2023,e,0,1)},F(xs,"XMLTypePackageImpl/5",1856),D(1901,1,si,jJ),l.wj=function(e){return _t(e,162)},l.xj=function(e){return Nt(Sv,ee,162,e,0,1)},F(xs,"XMLTypePackageImpl/50",1901),D(1902,1,si,M3),l.wj=function(e){return 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mc=Sr.collection(y.getAllInBox(sr[0],sr[1],sr[2],sr[3]));y.redrawHint("select",!0),mc.length>0&&y.redrawHint("eles",!0),Sr.emit({type:"boxend",originalEvent:Qt,position:{x:ir[0],y:ir[1]}});var Ta=function(qf){return qf.selectable()&&!qf.selected()};Sr.selectionType()==="additive"||Fo||Sr.$(g).unmerge(mc).unselect(),mc.emit("box").stdFilter(Ta).select().emit("boxselect"),y.redraw()}if(y.hoverData.dragging&&(y.hoverData.dragging=!1,y.redrawHint("select",!0),y.redrawHint("eles",!0),y.redraw()),!sr[4]){y.redrawHint("drag",!0),y.redrawHint("eles",!0);var Ja=Yi&&Yi.grabbed();dt($r),Ja&&(Yi.emit("freeon"),$r.emit("free"),y.dragData.didDrag&&(Yi.emit("dragfreeon"),$r.emit("dragfree")))}}sr[4]=0,y.hoverData.down=null,y.hoverData.cxtStarted=!1,y.hoverData.draggingEles=!1,y.hoverData.selecting=!1,y.hoverData.isOverThresholdDrag=!1,y.dragData.didDrag=!1,y.hoverData.dragged=!1,y.hoverData.dragDelta=[],y.hoverData.mdownPos=null,y.hoverData.mdownGPos=null}},!1);var ie=function(Qt){if(!y.scrollingPage){var jn=y.cy,Sr=jn.zoom(),ir=jn.pan(),sr=y.projectIntoViewport(Qt.clientX,Qt.clientY),Ia=[sr[0]*Sr+ir.x,sr[1]*Sr+ir.y];if(y.hoverData.draggingEles||y.hoverData.dragging||y.hoverData.cxtStarted||qt()){Qt.preventDefault();return}if(jn.panningEnabled()&&jn.userPanningEnabled()&&jn.zoomingEnabled()&&jn.userZoomingEnabled()){Qt.preventDefault(),y.data.wheelZooming=!0,clearTimeout(y.data.wheelTimeout),y.data.wheelTimeout=setTimeout(function(){y.data.wheelZooming=!1,y.redrawHint("eles",!0),y.redraw()},150);var $r;Qt.deltaY!=null?$r=Qt.deltaY/-250:Qt.wheelDeltaY!=null?$r=Qt.wheelDeltaY/1e3:$r=Qt.wheelDelta/1e3,$r=$r*y.wheelSensitivity;var Yi=Qt.deltaMode===1;Yi&&($r*=33);var 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0?(Sr[0]=(sr[0]+sr[2]+sr[4])/3,Sr[1]=(sr[1]+sr[3]+sr[5])/3,Sr[2]=(sr[0]+sr[2]+sr[4])/3+1,Sr[3]=(sr[1]+sr[3]+sr[5])/3+1):(Sr[2]=(sr[0]+sr[2]+sr[4])/3,Sr[3]=(sr[1]+sr[3]+sr[5])/3),y.redrawHint("select",!0),y.redraw();else if(jn&&Qt.touches[1]&&!y.touchData.didSelect&&ir.zoomingEnabled()&&ir.panningEnabled()&&ir.userZoomingEnabled()&&ir.userPanningEnabled()){Qt.preventDefault(),y.data.bgActivePosistion=void 0,y.redrawHint("select",!0);var y1=y.dragData.touchDragEles;if(y1){y.redrawHint("drag",!0);for(var Vd=0;Vd0&&!y.hoverData.draggingEles&&!y.swipePanning&&y.data.bgActivePosistion!=null&&(y.data.bgActivePosistion=void 0,y.redrawHint("select",!0),y.redraw())}},!1);var Jr;y.registerBinding(window,"touchcancel",Jr=function(Qt){var jn=y.touchData.start;y.touchData.capture=!1,jn&&jn.unactivate()});var vi,Xs,Ea,Ci;if(y.registerBinding(window,"touchend",vi=function(Qt){var jn=y.touchData.start,Sr=y.touchData.capture;if(Sr)Qt.touches.length===0&&(y.touchData.capture=!1),Qt.preventDefault();else return;var ir=y.selection;y.swipePanning=!1,y.hoverData.draggingEles=!1;var sr=y.cy,Ia=sr.zoom(),$r=y.touchData.now,Yi=y.touchData.earlier;if(Qt.touches[0]){var Fo=y.projectIntoViewport(Qt.touches[0].clientX,Qt.touches[0].clientY);$r[0]=Fo[0],$r[1]=Fo[1]}if(Qt.touches[1]){var Fo=y.projectIntoViewport(Qt.touches[1].clientX,Qt.touches[1].clientY);$r[2]=Fo[0],$r[3]=Fo[1]}if(Qt.touches[2]){var Fo=y.projectIntoViewport(Qt.touches[2].clientX,Qt.touches[2].clientY);$r[4]=Fo[0],$r[5]=Fo[1]}jn&&jn.unactivate();var Pc;if(y.touchData.cxt){if(Pc={originalEvent:Qt,type:"cxttapend",position:{x:$r[0],y:$r[1]}},jn?jn.emit(Pc):sr.emit(Pc),!y.touchData.cxtDragged){var Za={originalEvent:Qt,type:"cxttap",position:{x:$r[0],y:$r[1]}};jn?jn.emit(Za):sr.emit(Za)}y.touchData.start&&(y.touchData.start._private.grabbed=!1),y.touchData.cxt=!1,y.touchData.start=null,y.redraw();return}if(!Qt.touches[2]&&sr.boxSelectionEnabled()&&y.touchData.selecting){y.touchData.selecting=!1;var mc=sr.collection(y.getAllInBox(ir[0],ir[1],ir[2],ir[3]));ir[0]=void 0,ir[1]=void 0,ir[2]=void 0,ir[3]=void 0,ir[4]=0,y.redrawHint("select",!0),sr.emit({type:"boxend",originalEvent:Qt,position:{x:$r[0],y:$r[1]}});var Ta=function(F3){return F3.selectable()&&!F3.selected()};mc.emit("box").stdFilter(Ta).select().emit("boxselect"),mc.nonempty()&&y.redrawHint("eles",!0),y.redraw()}if(jn!=null&&jn.unactivate(),Qt.touches[2])y.data.bgActivePosistion=void 0,y.redrawHint("select",!0);else if(!Qt.touches[1]){if(!Qt.touches[0]){if(!Qt.touches[0]){y.data.bgActivePosistion=void 0,y.redrawHint("select",!0);var Ja=y.dragData.touchDragEles;if(jn!=null){var ml=jn._private.grabbed;dt(Ja),y.redrawHint("drag",!0),y.redrawHint("eles",!0),ml&&(jn.emit("freeon"),Ja.emit("free"),y.dragData.didDrag&&(jn.emit("dragfreeon"),Ja.emit("dragfree"))),x(jn,["touchend","tapend","vmouseup","tapdragout"],Qt,{x:$r[0],y:$r[1]}),jn.unactivate(),y.touchData.start=null}else{var qf=y.findNearestElement($r[0],$r[1],!0,!0);x(qf,["touchend","tapend","vmouseup","tapdragout"],Qt,{x:$r[0],y:$r[1]})}var Cp=y.touchData.startPosition[0]-$r[0],_p=Cp*Cp,Hf=y.touchData.startPosition[1]-$r[1],_g=Hf*Hf,cd=_p+_g,mw=cd*Ia*Ia;y.touchData.singleTouchMoved||(jn||sr.$(":selected").unselect(["tapunselect"]),x(jn,["tap","vclick"],Qt,{x:$r[0],y:$r[1]}),Xs=!1,Qt.timeStamp-Ci<=sr.multiClickDebounceTime()?(Ea&&clearTimeout(Ea),Xs=!0,Ci=null,x(jn,["dbltap","vdblclick"],Qt,{x:$r[0],y:$r[1]})):(Ea=setTimeout(function(){Xs||x(jn,["onetap","voneclick"],Qt,{x:$r[0],y:$r[1]})},sr.multiClickDebounceTime()),Ci=Qt.timeStamp)),jn!=null&&!y.dragData.didDrag&&jn._private.selectable&&mw"u"){var hi=[],gs=function(Qt){return{clientX:Qt.clientX,clientY:Qt.clientY,force:1,identifier:Qt.pointerId,pageX:Qt.pageX,pageY:Qt.pageY,radiusX:Qt.width/2,radiusY:Qt.height/2,screenX:Qt.screenX,screenY:Qt.screenY,target:Qt.target}},qi=function(Qt){return{event:Qt,touch:gs(Qt)}},Si=function(Qt){hi.push(qi(Qt))},Ui=function(Qt){for(var jn=0;jn0)return Sn[0]}return null},ot=Object.keys(Y),ht=0;ht0?rt:fN(O,P,g,x,T,L,$)},checkPoint:function(g,x,T,L,O,P,$){var q=Lk(L,O),S=2*q;if(dw(g,x,this.points,P,$,L,O-S,[0,-1],T)||dw(g,x,this.points,P,$,L-S,O,[0,-1],T))return!0;var V=L/2+2*T,Y=O/2+2*T,rt=[P-V,$-Y,P-V,$,P+V,$,P+V,$-Y];return!!(qd(g,x,rt)||S3(g,x,S,S,P+L/2-q,$+O/2-q,T)||S3(g,x,S,S,P-L/2+q,$+O/2-q,T))}}},bw.registerNodeShapes=function(){var y=this.nodeShapes={},g=this;this.generateEllipse(),this.generatePolygon("triangle",sd(3,0)),this.generateRoundPolygon("round-triangle",sd(3,0)),this.generatePolygon("rectangle",sd(4,0)),y.square=y.rectangle,this.generateRoundRectangle(),this.generateCutRectangle(),this.generateBarrel(),this.generateBottomRoundrectangle();{var x=[0,1,1,0,0,-1,-1,0];this.generatePolygon("diamond",x),this.generateRoundPolygon("round-diamond",x)}this.generatePolygon("pentagon",sd(5,0)),this.generateRoundPolygon("round-pentagon",sd(5,0)),this.generatePolygon("hexagon",sd(6,0)),this.generateRoundPolygon("round-hexagon",sd(6,0)),this.generatePolygon("heptagon",sd(7,0)),this.generateRoundPolygon("round-heptagon",sd(7,0)),this.generatePolygon("octagon",sd(8,0)),this.generateRoundPolygon("round-octagon",sd(8,0));var T=new Array(20);{var L=ML(5,0),O=ML(5,Math.PI/5),P=.5*(3-Math.sqrt(5));P*=1.57;for(var $=0;$=g.deqFastCost*$t)break}else if(S){if(Dt>=g.deqCost*ot||Dt>=g.deqAvgCost*rt)break}else if(Pt>=g.deqNoDrawCost*rM)break;var Zt=g.deq(T,Lt,dt);if(Zt.length>0)for(var Yt=0;Yt0&&(g.onDeqd(T,ht),!S&&g.shouldRedraw(T,ht,Lt,dt)&&O())},$=g.priority||EL;L.beforeRender(P,$(T))}}}},dtt=function(){function y(g){var x=arguments.length>1&&arguments[1]!==void 0?arguments[1]:wm;p(this,y),this.idsByKey=new Gb,this.keyForId=new Gb,this.cachesByLvl=new Gb,this.lvls=[],this.getKey=g,this.doesEleInvalidateKey=x}return m(y,[{key:"getIdsFor",value:function(x){x==null&&vl("Can not get id list for null key");var T=this.idsByKey,L=this.idsByKey.get(x);return L||(L=new Y5,T.set(x,L)),L}},{key:"addIdForKey",value:function(x,T){x!=null&&this.getIdsFor(x).add(T)}},{key:"deleteIdForKey",value:function(x,T){x!=null&&this.getIdsFor(x).delete(T)}},{key:"getNumberOfIdsForKey",value:function(x){return x==null?0:this.getIdsFor(x).size}},{key:"updateKeyMappingFor",value:function(x){var T=x.id(),L=this.keyForId.get(T),O=this.getKey(x);this.deleteIdForKey(L,T),this.addIdForKey(O,T),this.keyForId.set(T,O)}},{key:"deleteKeyMappingFor",value:function(x){var T=x.id(),L=this.keyForId.get(T);this.deleteIdForKey(L,T),this.keyForId.delete(T)}},{key:"keyHasChangedFor",value:function(x){var T=x.id(),L=this.keyForId.get(T),O=this.getKey(x);return L!==O}},{key:"isInvalid",value:function(x){return this.keyHasChangedFor(x)||this.doesEleInvalidateKey(x)}},{key:"getCachesAt",value:function(x){var T=this.cachesByLvl,L=this.lvls,O=T.get(x);return O||(O=new Gb,T.set(x,O),L.push(x)),O}},{key:"getCache",value:function(x,T){return this.getCachesAt(T).get(x)}},{key:"get",value:function(x,T){var L=this.getKey(x),O=this.getCache(L,T);return O!=null&&this.updateKeyMappingFor(x),O}},{key:"getForCachedKey",value:function(x,T){var L=this.keyForId.get(x.id()),O=this.getCache(L,T);return O}},{key:"hasCache",value:function(x,T){return this.getCachesAt(T).has(x)}},{key:"has",value:function(x,T){var L=this.getKey(x);return this.hasCache(L,T)}},{key:"setCache",value:function(x,T,L){L.key=x,this.getCachesAt(T).set(x,L)}},{key:"set",value:function(x,T,L){var O=this.getKey(x);this.setCache(O,T,L),this.updateKeyMappingFor(x)}},{key:"deleteCache",value:function(x,T){this.getCachesAt(T).delete(x)}},{key:"delete",value:function(x,T){var L=this.getKey(x);this.deleteCache(L,T)}},{key:"invalidateKey",value:function(x){var T=this;this.lvls.forEach(function(L){return T.deleteCache(x,L)})}},{key:"invalidate",value:function(x){var T=x.id(),L=this.keyForId.get(T);this.deleteKeyMappingFor(x);var O=this.doesEleInvalidateKey(x);return O&&this.invalidateKey(L),O||this.getNumberOfIdsForKey(L)===0}}]),y}(),xC=25,kC=50,px=-4,iM=3,sM=7.99,gtt=8,ptt=1024,btt=1024,rR=1024,wtt=.2,vtt=.8,mtt=10,ytt=.15,xtt=.1,ktt=.9,Ett=.9,Ttt=100,Ctt=1,bx={dequeue:"dequeue",downscale:"downscale",highQuality:"highQuality"},_tt=Rf({getKey:null,doesEleInvalidateKey:wm,drawElement:null,getBoundingBox:null,getRotationPoint:null,getRotationOffset:null,isVisible:T3,allowEdgeTxrCaching:!0,allowParentTxrCaching:!0}),Kk=function(g,x){var T=this;T.renderer=g,T.onDequeues=[];var L=_tt(x);de(T,L),T.lookup=new dtt(L.getKey,L.doesEleInvalidateKey),T.setupDequeueing()},Th=Kk.prototype;Th.reasons=bx,Th.getTextureQueue=function(y){var g=this;return g.eleImgCaches=g.eleImgCaches||{},g.eleImgCaches[y]=g.eleImgCaches[y]||[]},Th.getRetiredTextureQueue=function(y){var g=this,x=g.eleImgCaches.retired=g.eleImgCaches.retired||{},T=x[y]=x[y]||[];return T},Th.getElementQueue=function(){var y=this,g=y.eleCacheQueue=y.eleCacheQueue||new Ck(function(x,T){return T.reqs-x.reqs});return g},Th.getElementKeyToQueue=function(){var y=this,g=y.eleKeyToCacheQueue=y.eleKeyToCacheQueue||{};return g},Th.getElement=function(y,g,x,T,L){var O=this,P=this.renderer,$=P.cy.zoom(),q=this.lookup;if(!g||g.w===0||g.h===0||isNaN(g.w)||isNaN(g.h)||!y.visible()||y.removed()||!O.allowEdgeTxrCaching&&y.isEdge()||!O.allowParentTxrCaching&&y.isParent())return null;if(T==null&&(T=Math.ceil(_L($*x))),T=sM||T>iM)return null;var S=Math.pow(2,T),V=g.h*S,Y=g.w*S,rt=P.eleTextBiggerThanMin(y,S);if(!this.isVisible(y,rt))return null;var ot=q.get(y,T);if(ot&&ot.invalidated&&(ot.invalidated=!1,ot.texture.invalidatedWidth-=ot.width),ot)return ot;var ht;if(V<=xC?ht=xC:V<=kC?ht=kC:ht=Math.ceil(V/kC)*kC,V>rR||Y>btt)return null;var dt=O.getTextureQueue(ht),Lt=dt[dt.length-2],kt=function(){return O.recycleTexture(ht,Y)||O.addTexture(ht,Y)};Lt||(Lt=dt[dt.length-1]),Lt||(Lt=kt()),Lt.width-Lt.usedWidthT;be--)Gt=O.getElement(y,g,x,be,bx.downscale);ge()}else return O.queueElement(y,Yt.level-1),Yt;else{var ie;if(!Pt&&!$t&&!Zt)for(var Fe=T-1;Fe>=px;Fe--){var we=q.get(y,Fe);if(we){ie=we;break}}if(Dt(ie))return O.queueElement(y,T),ie;Lt.context.translate(Lt.usedWidth,0),Lt.context.scale(S,S),this.drawElement(Lt.context,y,g,rt,!1),Lt.context.scale(1/S,1/S),Lt.context.translate(-Lt.usedWidth,0)}return ot={x:Lt.usedWidth,texture:Lt,level:T,scale:S,width:Y,height:V,scaledLabelShown:rt},Lt.usedWidth+=Math.ceil(Y+gtt),Lt.eleCaches.push(ot),q.set(y,T,ot),O.checkTextureFullness(Lt),ot},Th.invalidateElements=function(y){for(var g=0;g=wtt*y.width&&this.retireTexture(y)},Th.checkTextureFullness=function(y){var g=this,x=g.getTextureQueue(y.height);y.usedWidth/y.width>vtt&&y.fullnessChecks>=mtt?vm(x,y):y.fullnessChecks++},Th.retireTexture=function(y){var g=this,x=y.height,T=g.getTextureQueue(x),L=this.lookup;vm(T,y),y.retired=!0;for(var O=y.eleCaches,P=0;P=g)return P.retired=!1,P.usedWidth=0,P.invalidatedWidth=0,P.fullnessChecks=0,TL(P.eleCaches),P.context.setTransform(1,0,0,1,0,0),P.context.clearRect(0,0,P.width,P.height),vm(L,P),T.push(P),P}},Th.queueElement=function(y,g){var x=this,T=x.getElementQueue(),L=x.getElementKeyToQueue(),O=this.getKey(y),P=L[O];if(P)P.level=Math.max(P.level,g),P.eles.merge(y),P.reqs++,T.updateItem(P);else{var $={eles:y.spawn().merge(y),level:g,reqs:1,key:O};T.push($),L[O]=$}},Th.dequeue=function(y){for(var g=this,x=g.getElementQueue(),T=g.getElementKeyToQueue(),L=[],O=g.lookup,P=0;P0;P++){var $=x.pop(),q=$.key,S=$.eles[0],V=O.hasCache(S,$.level);if(T[q]=null,V)continue;L.push($);var Y=g.getBoundingBox(S);g.getElement(S,Y,y,$.level,bx.dequeue)}return L},Th.removeFromQueue=function(y){var g=this,x=g.getElementQueue(),T=g.getElementKeyToQueue(),L=this.getKey(y),O=T[L];O!=null&&(O.eles.length===1?(O.reqs=W5,x.updateItem(O),x.pop(),T[L]=null):O.eles.unmerge(y))},Th.onDequeue=function(y){this.onDequeues.push(y)},Th.offDequeue=function(y){vm(this.onDequeues,y)},Th.setupDequeueing=yC.setupDequeueing({deqRedrawThreshold:Ttt,deqCost:ytt,deqAvgCost:xtt,deqNoDrawCost:ktt,deqFastCost:Ett,deq:function(g,x,T){return g.dequeue(x,T)},onDeqd:function(g,x){for(var T=0;T=EC||x>Xk)return null}T.validateLayersElesOrdering(x,y);var q=T.layersByLevel,S=Math.pow(2,x),V=q[x]=q[x]||[],Y,rt=T.levelIsComplete(x,y),ot,ht=function(){var ge=function(bn){if(T.validateLayersElesOrdering(bn,y),T.levelIsComplete(bn,y))return ot=q[bn],!0},be=function(bn){if(!ot)for(var ze=x+bn;wx<=ze&&ze<=Xk&&!ge(ze);ze+=bn);};be(1),be(-1);for(var ie=V.length-1;ie>=0;ie--){var Fe=V[ie];Fe.invalid&&vm(V,Fe)}};if(!rt)ht();else return V;var dt=function(){if(!Y){Y=zd();for(var ge=0;gefpt)return null;var Fe=T.makeLayer(Y,x);if(be!=null){var we=V.indexOf(be)+1;V.splice(we,0,Fe)}else(ge.insert===void 0||ge.insert)&&V.unshift(Fe);return Fe};if(T.skipping&&!$)return null;for(var kt=null,Dt=y.length/Stt,Pt=!$,$t=0;$t=Dt||!hN(kt.bb,Zt.boundingBox()))&&(kt=Lt({insert:!0,after:kt}),!kt))return null;ot||Pt?T.queueLayer(kt,Zt):T.drawEleInLayer(kt,Zt,x,g),kt.eles.push(Zt),qt[x]=kt}return ot||(Pt?null:V)},w1.getEleLevelForLayerLevel=function(y,g){return y},w1.drawEleInLayer=function(y,g,x,T){var L=this,O=this.renderer,P=y.context,$=g.boundingBox();$.w===0||$.h===0||!g.visible()||(x=L.getEleLevelForLayerLevel(x,T),O.setImgSmoothing(P,!1),O.drawCachedElement(P,g,null,null,x,dpt),O.setImgSmoothing(P,!0))},w1.levelIsComplete=function(y,g){var x=this,T=x.layersByLevel[y];if(!T||T.length===0)return!1;for(var L=0,O=0;O0||P.invalid)return!1;L+=P.eles.length}return L===g.length},w1.validateLayersElesOrdering=function(y,g){var x=this.layersByLevel[y];if(x)for(var T=0;T0){g=!0;break}}return g},w1.invalidateElements=function(y){var g=this;y.length!==0&&(g.lastInvalidationTime=yg(),!(y.length===0||!g.haveLayers())&&g.updateElementsInLayers(y,function(T,L,O){g.invalidateLayer(T)}))},w1.invalidateLayer=function(y){if(this.lastInvalidationTime=yg(),!y.invalid){var g=y.level,x=y.eles,T=this.layersByLevel[g];vm(T,y),y.elesQueue=[],y.invalid=!0,y.replacement&&(y.replacement.invalid=!0);for(var L=0;L3&&arguments[3]!==void 0?arguments[3]:!0,L=arguments.length>4&&arguments[4]!==void 0?arguments[4]:!0,O=arguments.length>5&&arguments[5]!==void 0?arguments[5]:!0,P=this,$=g._private.rscratch;if(!(O&&!g.visible())&&!($.badLine||$.allpts==null||isNaN($.allpts[0]))){var q;x&&(q=x,y.translate(-q.x1,-q.y1));var S=O?g.pstyle("opacity").value:1,V=O?g.pstyle("line-opacity").value:1,Y=g.pstyle("curve-style").value,rt=g.pstyle("line-style").value,ot=g.pstyle("width").pfValue,ht=g.pstyle("line-cap").value,dt=S*V,Lt=S*V,kt=function(){var ie=arguments.length>0&&arguments[0]!==void 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dt=g.pan(),Lt={x:dt.x*S,y:dt.y*S};S*=g.zoom(),ot.translate(Lt.x,Lt.y),ot.scale(S,S),this.drawElements(ot,ht),ot.scale(1/S,1/S),ot.translate(-Lt.x,-Lt.y)}y.bg&&(ot.globalCompositeOperation="destination-over",ot.fillStyle=y.bg,ot.rect(0,0,O,P),ot.fill())}return rt};function xpt(y,g){for(var x=atob(y),T=new ArrayBuffer(x.length),L=new Uint8Array(T),O=0;O"u"?"undefined":f(OffscreenCanvas))!=="undefined"?x=new OffscreenCanvas(y,g):(x=document.createElement("canvas"),x.width=y,x.height=g),x},[D0,ww,vw,CC,vx,Zk,Tg,O3,_C,$tt].forEach(function(y){de(vc,y)});var mx=[{name:"null",impl:WB},{name:"base",impl:nM},{name:"canvas",impl:kpt}],Cg=[{type:"layout",extensions:ltt},{type:"renderer",extensions:mx}],Sm={},cM={};function v1(y,g,x){var T=x,L=function(ne){Sc("Can not register `"+g+"` for `"+y+"` since `"+ne+"` already exists in the prototype and can not be overridden")};if(y==="core"){if(Vk.prototype[g])return L(g);Vk.prototype[g]=x}else if(y==="collection"){if($f.prototype[g])return L(g);$f.prototype[g]=x}else if(y==="layout"){for(var O=function(ne){this.options=ne,x.call(this,ne),ut(this._private)||(this._private={}),this._private.cy=ne.cy,this._private.listeners=[],this.createEmitter()},P=O.prototype=Object.create(x.prototype),$=[],q=0;q<$.length;q++){var S=$[q];P[S]=P[S]||function(){return this}}P.start&&!P.run?P.run=function(){return this.start(),this}:!P.start&&P.run&&(P.start=function(){return this.run(),this});var V=x.prototype.stop;P.stop=function(){var qt=this.options;if(qt&&qt.animate){var ne=this.animations;if(ne)for(var Gt=0;Gtz&&(this.rect.x-=(this.labelWidth-z)/2,this.setWidth(this.labelWidth)),this.labelHeight>W&&(this.labelPos=="center"?this.rect.y-=(this.labelHeight-W)/2:this.labelPos=="top"&&(this.rect.y-=this.labelHeight-W),this.setHeight(this.labelHeight))}}},B.prototype.getInclusionTreeDepth=function(){if(this.inclusionTreeDepth==b.MAX_VALUE)throw"assert failed";return this.inclusionTreeDepth},B.prototype.transform=function(R){var z=this.rect.x;z>_.WORLD_BOUNDARY?z=_.WORLD_BOUNDARY:z<-_.WORLD_BOUNDARY&&(z=-_.WORLD_BOUNDARY);var W=this.rect.y;W>_.WORLD_BOUNDARY?W=_.WORLD_BOUNDARY:W<-_.WORLD_BOUNDARY&&(W=-_.WORLD_BOUNDARY);var et=new I(z,W),st=R.inverseTransformPoint(et);this.setLocation(st.x,st.y)},B.prototype.getLeft=function(){return this.rect.x},B.prototype.getRight=function(){return this.rect.x+this.rect.width},B.prototype.getTop=function(){return this.rect.y},B.prototype.getBottom=function(){return this.rect.y+this.rect.height},B.prototype.getParent=function(){return this.owner==null?null:this.owner.getParent()},f.exports=B},function(f,p,w){function m(b,E){b==null&&E==null?(this.x=0,this.y=0):(this.x=b,this.y=E)}m.prototype.getX=function(){return this.x},m.prototype.getY=function(){return this.y},m.prototype.setX=function(b){this.x=b},m.prototype.setY=function(b){this.y=b},m.prototype.getDifference=function(b){return new DimensionD(this.x-b.x,this.y-b.y)},m.prototype.getCopy=function(){return new m(this.x,this.y)},m.prototype.translate=function(b){return this.x+=b.width,this.y+=b.height,this},f.exports=m},function(f,p,w){var m=w(2),b=w(10),E=w(0),_=w(6),A=w(3),I=w(1),B=w(13),N=w(12),R=w(11);function z(et,st,at){m.call(this,at),this.estimatedSize=b.MIN_VALUE,this.margin=E.DEFAULT_GRAPH_MARGIN,this.edges=[],this.nodes=[],this.isConnected=!1,this.parent=et,st!=null&&st instanceof _?this.graphManager=st:st!=null&&st instanceof Layout&&(this.graphManager=st.graphManager)}z.prototype=Object.create(m.prototype);for(var W in m)z[W]=m[W];z.prototype.getNodes=function(){return this.nodes},z.prototype.getEdges=function(){return this.edges},z.prototype.getGraphManager=function(){return this.graphManager},z.prototype.getParent=function(){return this.parent},z.prototype.getLeft=function(){return this.left},z.prototype.getRight=function(){return this.right},z.prototype.getTop=function(){return this.top},z.prototype.getBottom=function(){return this.bottom},z.prototype.isConnected=function(){return this.isConnected},z.prototype.add=function(et,st,at){if(st==null&&at==null){var bt=et;if(this.graphManager==null)throw"Graph has no graph mgr!";if(this.getNodes().indexOf(bt)>-1)throw"Node already in graph!";return bt.owner=this,this.getNodes().push(bt),bt}else{var mt=et;if(!(this.getNodes().indexOf(st)>-1&&this.getNodes().indexOf(at)>-1))throw"Source or target not in graph!";if(!(st.owner==at.owner&&st.owner==this))throw"Both owners must be this graph!";return st.owner!=at.owner?null:(mt.source=st,mt.target=at,mt.isInterGraph=!1,this.getEdges().push(mt),st.edges.push(mt),at!=st&&at.edges.push(mt),mt)}},z.prototype.remove=function(et){var st=et;if(et instanceof A){if(st==null)throw"Node is null!";if(!(st.owner!=null&&st.owner==this))throw"Owner graph is invalid!";if(this.graphManager==null)throw"Owner graph manager is invalid!";for(var at=st.edges.slice(),bt,mt=at.length,yt=0;yt-1&&vt>-1))throw"Source and/or target doesn't know this edge!";bt.source.edges.splice(ut,1),bt.target!=bt.source&&bt.target.edges.splice(vt,1);var ft=bt.source.owner.getEdges().indexOf(bt);if(ft==-1)throw"Not in owner's edge list!";bt.source.owner.getEdges().splice(ft,1)}},z.prototype.updateLeftTop=function(){for(var et=b.MAX_VALUE,st=b.MAX_VALUE,at,bt,mt,yt=this.getNodes(),ft=yt.length,ut=0;utat&&(et=at),st>bt&&(st=bt)}return et==b.MAX_VALUE?null:(yt[0].getParent().paddingLeft!=null?mt=yt[0].getParent().paddingLeft:mt=this.margin,this.left=st-mt,this.top=et-mt,new N(this.left,this.top))},z.prototype.updateBounds=function(et){for(var st=b.MAX_VALUE,at=-b.MAX_VALUE,bt=b.MAX_VALUE,mt=-b.MAX_VALUE,yt,ft,ut,vt,X,pt=this.nodes,U=pt.length,Tt=0;Ttyt&&(st=yt),atut&&(bt=ut),mtyt&&(st=yt),atut&&(bt=ut),mt=this.nodes.length){var U=0;at.forEach(function(Tt){Tt.owner==et&&U++}),U==this.nodes.length&&(this.isConnected=!0)}},f.exports=z},function(f,p,w){var m,b=w(1);function E(_){m=w(5),this.layout=_,this.graphs=[],this.edges=[]}E.prototype.addRoot=function(){var _=this.layout.newGraph(),A=this.layout.newNode(null),I=this.add(_,A);return this.setRootGraph(I),this.rootGraph},E.prototype.add=function(_,A,I,B,N){if(I==null&&B==null&&N==null){if(_==null)throw"Graph is null!";if(A==null)throw"Parent node is null!";if(this.graphs.indexOf(_)>-1)throw"Graph already in this graph mgr!";if(this.graphs.push(_),_.parent!=null)throw"Already has a parent!";if(A.child!=null)throw"Already has a child!";return _.parent=A,A.child=_,_}else{N=I,B=A,I=_;var R=B.getOwner(),z=N.getOwner();if(!(R!=null&&R.getGraphManager()==this))throw"Source not in this graph mgr!";if(!(z!=null&&z.getGraphManager()==this))throw"Target not in this graph mgr!";if(R==z)return I.isInterGraph=!1,R.add(I,B,N);if(I.isInterGraph=!0,I.source=B,I.target=N,this.edges.indexOf(I)>-1)throw"Edge already in inter-graph edge list!";if(this.edges.push(I),!(I.source!=null&&I.target!=null))throw"Edge source and/or target is null!";if(!(I.source.edges.indexOf(I)==-1&&I.target.edges.indexOf(I)==-1))throw"Edge already in source and/or target incidency list!";return I.source.edges.push(I),I.target.edges.push(I),I}},E.prototype.remove=function(_){if(_ instanceof m){var A=_;if(A.getGraphManager()!=this)throw"Graph not in this graph mgr";if(!(A==this.rootGraph||A.parent!=null&&A.parent.graphManager==this))throw"Invalid parent node!";var I=[];I=I.concat(A.getEdges());for(var B,N=I.length,R=0;R=_.getRight()?A[0]+=Math.min(_.getX()-E.getX(),E.getRight()-_.getRight()):_.getX()<=E.getX()&&_.getRight()>=E.getRight()&&(A[0]+=Math.min(E.getX()-_.getX(),_.getRight()-E.getRight())),E.getY()<=_.getY()&&E.getBottom()>=_.getBottom()?A[1]+=Math.min(_.getY()-E.getY(),E.getBottom()-_.getBottom()):_.getY()<=E.getY()&&_.getBottom()>=E.getBottom()&&(A[1]+=Math.min(E.getY()-_.getY(),_.getBottom()-E.getBottom()));var N=Math.abs((_.getCenterY()-E.getCenterY())/(_.getCenterX()-E.getCenterX()));_.getCenterY()===E.getCenterY()&&_.getCenterX()===E.getCenterX()&&(N=1);var R=N*A[0],z=A[1]/N;A[0]R)return A[0]=I,A[1]=W,A[2]=N,A[3]=pt,!1;if(BN)return A[0]=z,A[1]=B,A[2]=vt,A[3]=R,!1;if(IN?(A[0]=st,A[1]=at,It=!0):(A[0]=et,A[1]=W,It=!0):Bt===Z&&(I>N?(A[0]=z,A[1]=W,It=!0):(A[0]=bt,A[1]=at,It=!0)),-Et===Z?N>I?(A[2]=X,A[3]=pt,Ot=!0):(A[2]=vt,A[3]=ut,Ot=!0):Et===Z&&(N>I?(A[2]=ft,A[3]=ut,Ot=!0):(A[2]=U,A[3]=pt,Ot=!0)),It&&Ot)return!1;if(I>N?B>R?(Ct=this.getCardinalDirection(Bt,Z,4),xt=this.getCardinalDirection(Et,Z,2)):(Ct=this.getCardinalDirection(-Bt,Z,3),xt=this.getCardinalDirection(-Et,Z,1)):B>R?(Ct=this.getCardinalDirection(-Bt,Z,1),xt=this.getCardinalDirection(-Et,Z,3)):(Ct=this.getCardinalDirection(Bt,Z,2),xt=this.getCardinalDirection(Et,Z,4)),!It)switch(Ct){case 1:Le=W,Ht=I+-yt/Z,A[0]=Ht,A[1]=Le;break;case 2:Ht=bt,Le=B+mt*Z,A[0]=Ht,A[1]=Le;break;case 3:Le=at,Ht=I+yt/Z,A[0]=Ht,A[1]=Le;break;case 4:Ht=st,Le=B+-mt*Z,A[0]=Ht,A[1]=Le;break}if(!Ot)switch(xt){case 1:gn=ut,Ft=N+-nt/Z,A[2]=Ft,A[3]=gn;break;case 2:Ft=U,gn=R+Tt*Z,A[2]=Ft,A[3]=gn;break;case 3:gn=pt,Ft=N+nt/Z,A[2]=Ft,A[3]=gn;break;case 4:Ft=X,gn=R+-Tt*Z,A[2]=Ft,A[3]=gn;break}}return!1},b.getCardinalDirection=function(E,_,A){return E>_?A:1+A%4},b.getIntersection=function(E,_,A,I){if(I==null)return this.getIntersection2(E,_,A);var B=E.x,N=E.y,R=_.x,z=_.y,W=A.x,et=A.y,st=I.x,at=I.y,bt=void 0,mt=void 0,yt=void 0,ft=void 0,ut=void 0,vt=void 0,X=void 0,pt=void 0,U=void 0;return yt=z-N,ut=B-R,X=R*N-B*z,ft=at-et,vt=W-st,pt=st*et-W*at,U=yt*vt-ft*ut,U===0?null:(bt=(ut*pt-vt*X)/U,mt=(ft*X-yt*pt)/U,new m(bt,mt))},b.angleOfVector=function(E,_,A,I){var B=void 0;return E!==A?(B=Math.atan((I-_)/(A-E)),A0?1:b<0?-1:0},m.floor=function(b){return b<0?Math.ceil(b):Math.floor(b)},m.ceil=function(b){return b<0?Math.floor(b):Math.ceil(b)},f.exports=m},function(f,p,w){function m(){}m.MAX_VALUE=2147483647,m.MIN_VALUE=-2147483648,f.exports=m},function(f,p,w){var m=function(){function B(N,R){for(var z=0;z"u"?"undefined":m(E);return E==null||_!="object"&&_!="function"},f.exports=b},function(f,p,w){function m(W){if(Array.isArray(W)){for(var et=0,st=Array(W.length);et0&&et;){for(yt.push(ut[0]);yt.length>0&&et;){var vt=yt[0];yt.splice(0,1),mt.add(vt);for(var X=vt.getEdges(),bt=0;bt-1&&ut.splice(nt,1)}mt=new Set,ft=new Map}}return W},z.prototype.createDummyNodesForBendpoints=function(W){for(var et=[],st=W.source,at=this.graphManager.calcLowestCommonAncestor(W.source,W.target),bt=0;bt0){for(var at=this.edgeToDummyNodes.get(st),bt=0;bt=0&&et.splice(pt,1);var U=ft.getNeighborsList();U.forEach(function(It){if(st.indexOf(It)<0){var Ot=at.get(It),Bt=Ot-1;Bt==1&&vt.push(It),at.set(It,Bt)}})}st=st.concat(vt),(et.length==1||et.length==2)&&(bt=!0,mt=et[0])}return mt},z.prototype.setGraphManager=function(W){this.graphManager=W},f.exports=z},function(f,p,w){function m(){}m.seed=1,m.x=0,m.nextDouble=function(){return m.x=Math.sin(m.seed++)*1e4,m.x-Math.floor(m.x)},f.exports=m},function(f,p,w){var m=w(4);function b(E,_){this.lworldOrgX=0,this.lworldOrgY=0,this.ldeviceOrgX=0,this.ldeviceOrgY=0,this.lworldExtX=1,this.lworldExtY=1,this.ldeviceExtX=1,this.ldeviceExtY=1}b.prototype.getWorldOrgX=function(){return this.lworldOrgX},b.prototype.setWorldOrgX=function(E){this.lworldOrgX=E},b.prototype.getWorldOrgY=function(){return this.lworldOrgY},b.prototype.setWorldOrgY=function(E){this.lworldOrgY=E},b.prototype.getWorldExtX=function(){return this.lworldExtX},b.prototype.setWorldExtX=function(E){this.lworldExtX=E},b.prototype.getWorldExtY=function(){return this.lworldExtY},b.prototype.setWorldExtY=function(E){this.lworldExtY=E},b.prototype.getDeviceOrgX=function(){return this.ldeviceOrgX},b.prototype.setDeviceOrgX=function(E){this.ldeviceOrgX=E},b.prototype.getDeviceOrgY=function(){return this.ldeviceOrgY},b.prototype.setDeviceOrgY=function(E){this.ldeviceOrgY=E},b.prototype.getDeviceExtX=function(){return this.ldeviceExtX},b.prototype.setDeviceExtX=function(E){this.ldeviceExtX=E},b.prototype.getDeviceExtY=function(){return this.ldeviceExtY},b.prototype.setDeviceExtY=function(E){this.ldeviceExtY=E},b.prototype.transformX=function(E){var _=0,A=this.lworldExtX;return A!=0&&(_=this.ldeviceOrgX+(E-this.lworldOrgX)*this.ldeviceExtX/A),_},b.prototype.transformY=function(E){var _=0,A=this.lworldExtY;return A!=0&&(_=this.ldeviceOrgY+(E-this.lworldOrgY)*this.ldeviceExtY/A),_},b.prototype.inverseTransformX=function(E){var _=0,A=this.ldeviceExtX;return A!=0&&(_=this.lworldOrgX+(E-this.ldeviceOrgX)*this.lworldExtX/A),_},b.prototype.inverseTransformY=function(E){var _=0,A=this.ldeviceExtY;return A!=0&&(_=this.lworldOrgY+(E-this.ldeviceOrgY)*this.lworldExtY/A),_},b.prototype.inverseTransformPoint=function(E){var _=new m(this.inverseTransformX(E.x),this.inverseTransformY(E.y));return _},f.exports=b},function(f,p,w){function m(R){if(Array.isArray(R)){for(var z=0,W=Array(R.length);zE.ADAPTATION_LOWER_NODE_LIMIT&&(this.coolingFactor=Math.max(this.coolingFactor*E.COOLING_ADAPTATION_FACTOR,this.coolingFactor-(R-E.ADAPTATION_LOWER_NODE_LIMIT)/(E.ADAPTATION_UPPER_NODE_LIMIT-E.ADAPTATION_LOWER_NODE_LIMIT)*this.coolingFactor*(1-E.COOLING_ADAPTATION_FACTOR))),this.maxNodeDisplacement=E.MAX_NODE_DISPLACEMENT_INCREMENTAL):(R>E.ADAPTATION_LOWER_NODE_LIMIT?this.coolingFactor=Math.max(E.COOLING_ADAPTATION_FACTOR,1-(R-E.ADAPTATION_LOWER_NODE_LIMIT)/(E.ADAPTATION_UPPER_NODE_LIMIT-E.ADAPTATION_LOWER_NODE_LIMIT)*(1-E.COOLING_ADAPTATION_FACTOR)):this.coolingFactor=1,this.initialCoolingFactor=this.coolingFactor,this.maxNodeDisplacement=E.MAX_NODE_DISPLACEMENT),this.maxIterations=Math.max(this.getAllNodes().length*5,this.maxIterations),this.totalDisplacementThreshold=this.displacementThresholdPerNode*this.getAllNodes().length,this.repulsionRange=this.calcRepulsionRange()},B.prototype.calcSpringForces=function(){for(var R=this.getAllEdges(),z,W=0;W0&&arguments[0]!==void 0?arguments[0]:!0,z=arguments.length>1&&arguments[1]!==void 0?arguments[1]:!1,W,et,st,at,bt=this.getAllNodes(),mt;if(this.useFRGridVariant)for(this.totalIterations%E.GRID_CALCULATION_CHECK_PERIOD==1&&R&&this.updateGrid(),mt=new Set,W=0;Wyt||mt>yt)&&(R.gravitationForceX=-this.gravityConstant*st,R.gravitationForceY=-this.gravityConstant*at)):(yt=z.getEstimatedSize()*this.compoundGravityRangeFactor,(bt>yt||mt>yt)&&(R.gravitationForceX=-this.gravityConstant*st*this.compoundGravityConstant,R.gravitationForceY=-this.gravityConstant*at*this.compoundGravityConstant))},B.prototype.isConverged=function(){var R,z=!1;return this.totalIterations>this.maxIterations/3&&(z=Math.abs(this.totalDisplacement-this.oldTotalDisplacement)<2),R=this.totalDisplacement=bt.length||yt>=bt[0].length)){for(var ft=0;ftB}}]),A}();f.exports=_},function(f,p,w){var m=function(){function _(A,I){for(var B=0;B2&&arguments[2]!==void 0?arguments[2]:1,N=arguments.length>3&&arguments[3]!==void 0?arguments[3]:-1,R=arguments.length>4&&arguments[4]!==void 0?arguments[4]:-1;b(this,_),this.sequence1=A,this.sequence2=I,this.match_score=B,this.mismatch_penalty=N,this.gap_penalty=R,this.iMax=A.length+1,this.jMax=I.length+1,this.grid=new Array(this.iMax);for(var z=0;z=0;A--){var I=this.listeners[A];I.event===E&&I.callback===_&&this.listeners.splice(A,1)}},b.emit=function(E,_){for(var A=0;AI.coolingFactor*I.maxNodeDisplacement&&(this.displacementX=I.coolingFactor*I.maxNodeDisplacement*E.sign(this.displacementX)),Math.abs(this.displacementY)>I.coolingFactor*I.maxNodeDisplacement&&(this.displacementY=I.coolingFactor*I.maxNodeDisplacement*E.sign(this.displacementY)),this.child==null?this.moveBy(this.displacementX,this.displacementY):this.child.getNodes().length==0?this.moveBy(this.displacementX,this.displacementY):this.propogateDisplacementToChildren(this.displacementX,this.displacementY),I.totalDisplacement+=Math.abs(this.displacementX)+Math.abs(this.displacementY),this.springForceX=0,this.springForceY=0,this.repulsionForceX=0,this.repulsionForceY=0,this.gravitationForceX=0,this.gravitationForceY=0,this.displacementX=0,this.displacementY=0},_.prototype.propogateDisplacementToChildren=function(I,B){for(var N=this.getChild().getNodes(),R,z=0;z0)this.positionNodesRadially(ut);else{this.reduceTrees(),this.graphManager.resetAllNodesToApplyGravitation();var vt=new Set(this.getAllNodes()),X=this.nodesWithGravity.filter(function(pt){return vt.has(pt)});this.graphManager.setAllNodesToApplyGravitation(X),this.positionNodesRandomly()}}return this.initSpringEmbedder(),this.runSpringEmbedder(),!0},yt.prototype.tick=function(){if(this.totalIterations++,this.totalIterations===this.maxIterations&&!this.isTreeGrowing&&!this.isGrowthFinished)if(this.prunedNodesAll.length>0)this.isTreeGrowing=!0;else return!0;if(this.totalIterations%N.CONVERGENCE_CHECK_PERIOD==0&&!this.isTreeGrowing&&!this.isGrowthFinished){if(this.isConverged())if(this.prunedNodesAll.length>0)this.isTreeGrowing=!0;else return!0;this.coolingCycle++,this.layoutQuality==0?this.coolingAdjuster=this.coolingCycle:this.layoutQuality==1&&(this.coolingAdjuster=this.coolingCycle/3),this.coolingFactor=Math.max(this.initialCoolingFactor-Math.pow(this.coolingCycle,Math.log(100*(this.initialCoolingFactor-this.finalTemperature))/Math.log(this.maxCoolingCycle))/100*this.coolingAdjuster,this.finalTemperature),this.animationPeriod=Math.ceil(this.initialAnimationPeriod*Math.sqrt(this.coolingFactor))}if(this.isTreeGrowing){if(this.growTreeIterations%10==0)if(this.prunedNodesAll.length>0){this.graphManager.updateBounds(),this.updateGrid(),this.growTree(this.prunedNodesAll),this.graphManager.resetAllNodesToApplyGravitation();var ut=new Set(this.getAllNodes()),vt=this.nodesWithGravity.filter(function(U){return ut.has(U)});this.graphManager.setAllNodesToApplyGravitation(vt),this.graphManager.updateBounds(),this.updateGrid(),this.coolingFactor=N.DEFAULT_COOLING_FACTOR_INCREMENTAL}else this.isTreeGrowing=!1,this.isGrowthFinished=!0;this.growTreeIterations++}if(this.isGrowthFinished){if(this.isConverged())return!0;this.afterGrowthIterations%10==0&&(this.graphManager.updateBounds(),this.updateGrid()),this.coolingFactor=N.DEFAULT_COOLING_FACTOR_INCREMENTAL*((100-this.afterGrowthIterations)/100),this.afterGrowthIterations++}var X=!this.isTreeGrowing&&!this.isGrowthFinished,pt=this.growTreeIterations%10==1&&this.isTreeGrowing||this.afterGrowthIterations%10==1&&this.isGrowthFinished;return this.totalDisplacement=0,this.graphManager.updateBounds(),this.calcSpringForces(),this.calcRepulsionForces(X,pt),this.calcGravitationalForces(),this.moveNodes(),this.animate(),!1},yt.prototype.getPositionsData=function(){for(var ut=this.graphManager.getAllNodes(),vt={},X=0;X1){var It;for(It=0;Itpt&&(pt=Math.floor(nt.y)),Tt=Math.floor(nt.x+B.DEFAULT_COMPONENT_SEPERATION)}this.transform(new W(R.WORLD_CENTER_X-nt.x/2,R.WORLD_CENTER_Y-nt.y/2))},yt.radialLayout=function(ut,vt,X){var pt=Math.max(this.maxDiagonalInTree(ut),B.DEFAULT_RADIAL_SEPARATION);yt.branchRadialLayout(vt,null,0,359,0,pt);var U=bt.calculateBounds(ut),Tt=new mt;Tt.setDeviceOrgX(U.getMinX()),Tt.setDeviceOrgY(U.getMinY()),Tt.setWorldOrgX(X.x),Tt.setWorldOrgY(X.y);for(var nt=0;nt1;){var gn=Ft[0];Ft.splice(0,1);var Se=Z.indexOf(gn);Se>=0&&Z.splice(Se,1),Ht--,Ct--}vt!=null?Le=(Z.indexOf(Ft[0])+1)%Ht:Le=0;for(var me=Math.abs(pt-X)/Ct,Ve=Le;xt!=Ct;Ve=++Ve%Ht){var Ye=Z[Ve].getOtherEnd(ut);if(Ye!=vt){var ce=(X+xt*me)%360,ke=(ce+me)%360;yt.branchRadialLayout(Ye,ut,ce,ke,U+Tt,Tt),xt++}}},yt.maxDiagonalInTree=function(ut){for(var vt=st.MIN_VALUE,X=0;Xvt&&(vt=U)}return vt},yt.prototype.calcRepulsionRange=function(){return 2*(this.level+1)*this.idealEdgeLength},yt.prototype.groupZeroDegreeMembers=function(){var ut=this,vt={};this.memberGroups={},this.idToDummyNode={};for(var X=[],pt=this.graphManager.getAllNodes(),U=0;U"u"&&(vt[It]=[]),vt[It]=vt[It].concat(Tt)}Object.keys(vt).forEach(function(Ot){if(vt[Ot].length>1){var Bt="DummyCompound_"+Ot;ut.memberGroups[Bt]=vt[Ot];var Et=vt[Ot][0].getParent(),Z=new A(ut.graphManager);Z.id=Bt,Z.paddingLeft=Et.paddingLeft||0,Z.paddingRight=Et.paddingRight||0,Z.paddingBottom=Et.paddingBottom||0,Z.paddingTop=Et.paddingTop||0,ut.idToDummyNode[Bt]=Z;var Ct=ut.getGraphManager().add(ut.newGraph(),Z),xt=Et.getChild();xt.add(Z);for(var Ht=0;Ht=0;ut--){var vt=this.compoundOrder[ut],X=vt.id,pt=vt.paddingLeft,U=vt.paddingTop;this.adjustLocations(this.tiledMemberPack[X],vt.rect.x,vt.rect.y,pt,U)}},yt.prototype.repopulateZeroDegreeMembers=function(){var ut=this,vt=this.tiledZeroDegreePack;Object.keys(vt).forEach(function(X){var pt=ut.idToDummyNode[X],U=pt.paddingLeft,Tt=pt.paddingTop;ut.adjustLocations(vt[X],pt.rect.x,pt.rect.y,U,Tt)})},yt.prototype.getToBeTiled=function(ut){var vt=ut.id;if(this.toBeTiled[vt]!=null)return this.toBeTiled[vt];var X=ut.getChild();if(X==null)return this.toBeTiled[vt]=!1,!1;for(var pt=X.getNodes(),U=0;U0)return this.toBeTiled[vt]=!1,!1;if(Tt.getChild()==null){this.toBeTiled[Tt.id]=!1;continue}if(!this.getToBeTiled(Tt))return this.toBeTiled[vt]=!1,!1}return this.toBeTiled[vt]=!0,!0},yt.prototype.getNodeDegree=function(ut){ut.id;for(var vt=ut.getEdges(),X=0,pt=0;ptOt&&(Ot=Et.rect.height)}X+=Ot+ut.verticalPadding}},yt.prototype.tileCompoundMembers=function(ut,vt){var X=this;this.tiledMemberPack=[],Object.keys(ut).forEach(function(pt){var U=vt[pt];X.tiledMemberPack[pt]=X.tileNodes(ut[pt],U.paddingLeft+U.paddingRight),U.rect.width=X.tiledMemberPack[pt].width,U.rect.height=X.tiledMemberPack[pt].height})},yt.prototype.tileNodes=function(ut,vt){var X=B.TILING_PADDING_VERTICAL,pt=B.TILING_PADDING_HORIZONTAL,U={rows:[],rowWidth:[],rowHeight:[],width:0,height:vt,verticalPadding:X,horizontalPadding:pt};ut.sort(function(It,Ot){return It.rect.width*It.rect.height>Ot.rect.width*Ot.rect.height?-1:It.rect.width*It.rect.height0&&(nt+=ut.horizontalPadding),ut.rowWidth[X]=nt,ut.width0&&(It+=ut.verticalPadding);var Ot=0;It>ut.rowHeight[X]&&(Ot=ut.rowHeight[X],ut.rowHeight[X]=It,Ot=ut.rowHeight[X]-Ot),ut.height+=Ot,ut.rows[X].push(vt)},yt.prototype.getShortestRowIndex=function(ut){for(var vt=-1,X=Number.MAX_VALUE,pt=0;ptX&&(vt=pt,X=ut.rowWidth[pt]);return vt},yt.prototype.canAddHorizontal=function(ut,vt,X){var pt=this.getShortestRowIndex(ut);if(pt<0)return!0;var U=ut.rowWidth[pt];if(U+ut.horizontalPadding+vt<=ut.width)return!0;var Tt=0;ut.rowHeight[pt]0&&(Tt=X+ut.verticalPadding-ut.rowHeight[pt]);var nt;ut.width-U>=vt+ut.horizontalPadding?nt=(ut.height+Tt)/(U+vt+ut.horizontalPadding):nt=(ut.height+Tt)/ut.width,Tt=X+ut.verticalPadding;var It;return ut.widthTt&&vt!=X){pt.splice(-1,1),ut.rows[X].push(U),ut.rowWidth[vt]=ut.rowWidth[vt]-Tt,ut.rowWidth[X]=ut.rowWidth[X]+Tt,ut.width=ut.rowWidth[instance.getLongestRowIndex(ut)];for(var nt=Number.MIN_VALUE,It=0;Itnt&&(nt=pt[It].height);vt>0&&(nt+=ut.verticalPadding);var Ot=ut.rowHeight[vt]+ut.rowHeight[X];ut.rowHeight[vt]=nt,ut.rowHeight[X]0)for(var xt=U;xt<=Tt;xt++)Ct[0]+=this.grid[xt][nt-1].length+this.grid[xt][nt].length-1;if(Tt0)for(var xt=nt;xt<=It;xt++)Ct[3]+=this.grid[U-1][xt].length+this.grid[U][xt].length-1;for(var Ht=st.MAX_VALUE,Le,Ft,gn=0;gn0){var It;It=mt.getGraphManager().add(mt.newGraph(),X),this.processChildrenList(It,vt,mt)}}},W.prototype.stop=function(){return this.stopped=!0,this};var st=function(bt){bt("layout","cose-bilkent",W)};typeof cytoscape<"u"&&st(cytoscape),p.exports=st}])})})(h$t);var uYe=h$t.exports;const lYe=G7(uYe);l$t.use(lYe);function g$t(i,a,f,p){c$t.drawNode(i,a,f,p),a.children&&a.children.forEach((w,m)=>{g$t(i,w,f<0?m:f,p)})}function hYe(i,a){a.edges().map((f,p)=>{const w=f.data();if(f[0]._private.bodyBounds){const m=f[0]._private.rscratch;Ut.trace("Edge: ",p,w),i.insert("path").attr("d",`M ${m.startX},${m.startY} L ${m.midX},${m.midY} L${m.endX},${m.endY} `).attr("class","edge section-edge-"+w.section+" edge-depth-"+w.depth)}})}function p$t(i,a,f,p){a.add({group:"nodes",data:{id:i.id,labelText:i.descr,height:i.height,width:i.width,level:p,nodeId:i.id,padding:i.padding,type:i.type},position:{x:i.x,y:i.y}}),i.children&&i.children.forEach(w=>{p$t(w,a,f,p+1),a.add({group:"edges",data:{id:`${i.id}_${w.id}`,source:i.id,target:w.id,depth:p,section:w.section}})})}function fYe(i,a){return new Promise(f=>{const p=yr("body").append("div").attr("id","cy").attr("style","display:none"),w=l$t({container:document.getElementById("cy"),style:[{selector:"edge",style:{"curve-style":"bezier"}}]});p.remove(),p$t(i,w,a,0),w.nodes().forEach(function(m){m.layoutDimensions=()=>{const 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0,_,w.mindmap.padding,w.mindmap.useMaxWidth)}},pYe=i=>{let a="";for(let f=0;f` + .edge { + stroke-width: 3; + } + ${pYe(i)} + .section-root rect, .section-root path, .section-root circle, .section-root polygon { + fill: ${i.git0}; + } + .section-root text { + fill: ${i.gitBranchLabel0}; + } + .icon-container { + height:100%; + display: flex; + justify-content: center; + align-items: center; + } + .edge { + fill: none; + } + .mindmap-node-label { + dy: 1em; + alignment-baseline: middle; + text-anchor: middle; + dominant-baseline: middle; + text-align: center; + } +`}},Symbol.toStringTag,{value:"Module"}));var npt=function(){var i=function(E,_,A,I){for(A=A||{},I=E.length;I--;A[E[I]]=_);return 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+ + + + + + + + + + + + + + + + + + + +
+ +
+ + + + + + + + +
+
+

Notes taken @ ETH Zurich

+

Introduction

+

Here I list all courses I took at ETH Zurich and provide a brief overview of the course content. The clickable links will lead you to the respective course notes.

+

Courses are organized by semester and year. The course notes are organized by lecture.

+

22HS

+
    +
  • Computational Biology
    • +
  • Data Mining I
    • +
  • Information Systems for Engineers
    • +
  • Computational Systems Biology
    • +
+

23FS + HS

+ +

No courses (except for seminar) taken in 23HS since I was doing an internship at Roche.

+

24FS

+
    +
  • Biofluiddynamics
    • +
  • Synthetic Biology I
    • +
+

Mobile Health and Activity Monitoring

+

Functional Genomics

+

A course collectively taught by multiple professors. Multiple-choice exam, lots of memorization.

+

Table of Contents

+ + +

Modern Genomics I

+ +

Introduction

+

Molecular biology is governed by the "central dogma". Genomics is basically studying the DNA part of it.

+

Genome sequence: complete listing of all nucleotides of one organisms, in correct order, and mapped to the chromosomes.

+
graph LR
+    A[DNA] -->|Transcription| B[RNA]
+    B -->|Translation| C[Protein]
+
+

Timeline

+

Efficient sequencing technology arrived rather late. Initially the sequencing process was cumbersome and radioactive.

+
    +
  • 1975: "dideoxy" DNA sequencing (Sanger)
    • +
  • 1977: first genome (bacteriophage \( \phi X 174 \) )
    • +
  • 1995: first cell (Haemophilus influenzae)
    • +
  • 1998: first animal (Caenorhabditis elegans)
    • +
  • 2001: Homo sapiens
    • +
  • Today (February 2023) +
      +
    • genomes available for: 409,947 Bacteria, 4,988 Archaea, 47,200 Eukaryotes
      • +
    • human genomes fairly routine +
        +
      • below 1000$ raw costs
        • +
      • "Personal Genome Projects" are enrolling 100’000s of volunteers, including their medical records
        • +
      +
      • +
    +
    • +
+

Why Genomics?

+
    +
  • Because we want an inventory of all genes and functions
    • +
  • Because wea can compare genomes to learn about evolution, to get hints on gene function, etc +
      +
    • Comparison can be either based on DNA or protein
      • +
    • Alignments, dot plots, whole chromosome comparison
      • +
    +
    • +
+

Comparative genomics use case examples

+
    +
  • Gene prediction +
      +
    • Gene prediction algorithms that use homology (=comparative genomics result) information: SLAM, SGP, Twinscan (= N-SCAN)...
      • +
    • UCSC genome browser gene prediction
      • +
    +
    • +
  • Gene family evolution
    • +
+

Classical sequencing method

+

Sanger (double-deoxy) sequencing

+

Natural DNA extension requires 3'-OH. The dideoxy method uses a 2',3'-dideoxy nucleotide, which lacks the 3'-OH group. This causes the DNA chain to terminate. By introducing different dideoxy nucleotides, the sequence can be read.

+

Automated Dye Sequencing

+

Variants of Sanger sequencing. Still utilize the dideoxy method to terminate DNA elongation. The difference is that the dideoxy nucleotides are labeled with different fluorescent dyes. The sequence is read by a laser.

+

Two variants of Automated Dye Sequencing

+

Dye terminator sequencing is now widely used over the rather cumbersome (4 tubes per sample) dye primer chemistry.

+

New (Next-generation) sequencing technologies

+

Generally involves first amplifying the DNA, then sequencing it. Sequencing is done by detecting the nucleotides as they are incorporated into the growing DNA strand (sequencing by synthesis). High-throughput is achieved by parallelizing the sequencing process.

+

Amplification technologies

+

First-generation amplification technology: needs DNA-library in bacterial vectors --> cumbersome and biased

+

Improvement: get rid of bacteria

+

Emulsion PCR

+

Improvement: bacterium free, but still needs cloning

+
%%{init: {"graph": {"htmlLabels": false}} }%%
+graph TD
+    A["`**Fragment** the DNA, ligate **adapters** to ends, make **single-stranded**`"] --> B["Attach to microbeads"]
+    B --> C["`PCR-amplify, in a **water-oil emulsion**`"]
+    C --> D["`Enrich beads having successful amplifications, then place into regular lattice
+    (see figure below for details)`"]
+
+

Emulsion PCR enrichment step

+

In short, the enrichment is done by capturing the second (5'-end) primer of the PCR product onto a large polysyrene bead.

+

PCR on solid support

+

PCR on solid support

+

Barcoding and "linked reads"

+

Barcoding

+

10X technology

+

Sequencing technologies

+

First-generation sequencing needs DNA size-separation on a gel

+

Improvement: get rid of gel (sequencing by synthesis)

+

Pyrosequencing

+

Pyrosequencing

+

Reversible terminator sequencing

+

Reversible terminator sequencing

+

Sequencing by semi-conductor

+

Directly detects the release of H+ ions when a nucleotide is incorporated into the growing DNA strand.

+

Sequencing by semi-conductor

+

Current implementations of NGS

+
    +
  • Illumina +
      +
    • Illumina NovaSeq 6000
      • +
    • PCR on solid support
      • +
    • reversible terminator sequencing
      • +
    • read length ca. 250bp
      • +
    • 1e14 bp per run
      • +
    +
    • +
  • Ion Torrent / Life Techn. Inc +
      +
    • Ion Gene Studio S5
      • +
    • PCR on beads
      • +
    • sequencing by semi-conductor
      • +
    • read length ca. 600bp
      • +
    • 1e10 bp per run
      • +
    +
    • +
+

Third-generation sequencing technologies

+

Single molecule sequencing. No need for amplification.

+

Characterized by extremely long reads, but also high error rates.

+
    +
  • Pacific Biosciences +
      +
    • SMRT (single molecule real time) sequencing
      • +
    • pacbio1
      • +
    • pacbio1
      • +
    +
    • +
  • Oxford Nanopore +
      +
    • MinION
      • +
    • oxford nanopore
      • +
    +
    • +
+
+

Self-note: minimap2 is a popular aligner for long reads.

+
+

Environmental sequencing

+

Traditional genome sequencing requires individual cell isolation and cultivation. This is not possible for the majority of microorganisms. But one advantage is that it's possible to re-assemble the genome from the reads.

+

Environmental sequencing: directly sequence DNA extracted from the environment without purification and clonal cultivation. Genome assembly is generally not possible.

+
+

Self-note: data generated from environmental sequencing is typically large in size, but highly fragmented and contaminated. Lots of exciting research in this area.

+
+

How to deal with environmental sequencing data

+
    +
  • Novel gene discovery +
      +
    • Sequence identity comparison to known genes +
        +
      • But > 50% of the environmental genomes are not similar to any known genome
        • +
      +
      • +
    +
    • +
  • Novel gene families
    • +
  • Gene family clustering (similar samples have similar gene family distribution)
    • +
+

Single-cell sequencing

+

Why?

+
    +
  • Heterogeneity in cell populations +
      +
    • Tumor cells
      • +
    • Immune cells
      • +
    • Microbial communities
      • +
    • Developmental biology
      • +
    +
    • +
+

How?

+

In short, we first get single cells, then amplify the whole genome and sequence it.

+

The challenges lie in the bolded parts.

+

Single-cell isolation

+

(In the very first "single cell" genomics paper, the "single" cells were literally picked manually...nowadays we don't do that)

+
    +
  1. Sorting with optical tweezers +Optic tweezers
    2. +
  2. Dilution series
    3. +
  3. Flow sorting +Flow sorting
    4. +
+

Whole genome amplification

+

Steps summarized:

+
    +
  1. MDA
    2. +
  2. phi 29 debranching
    3. +
  3. S1 nuclease digestion
    4. +
  4. DNA pol I nick translation
    5. +
  5. Cloning
    6. +
+
    +
  • Isothermal Multiple displacement amplification (MDA) +
      +
    • Phi29 DNA polymerase
      • +
    • Random primers
      • +
    • Isothermal amplification
      • +
    +
    • +
+

MDA

+

After MDA, we obtained a "hyperbranched chromosome". After debranching and cloning, we can sequence and re-assemble the genome.

+

Next steps

+

The debranching is done by incubating phi 29 DNA pol with hyperbranched DNA without any primer. The strand-replacement activity of phi 29 DNA pol will remove the hyperbranched structure.

+

S1 nucleases are used to remove the remaining single-stranded DNA.

+

Nicks are filled in by DNA pol I (has 5'->3' exonuclease activity).

+

Genomic databases

+

This section likely won't be covered in the exam.

+
+

General popular resources:

+
    +
  • Raw data: NCBI sequence read archive (SRA) (also it's European counterpart, EBI European Nucleotide Archive (ENA), but they are basically the same thing now) +
      +
    • seq quality score included
      • +
    • but incomplete: legacy & newer data not available
      • +
    • gigantic in size
      • +
    +
    • +
  • Sequencing projects: GOLD (Genomes OnLine Database) +
      +
    • keep track of "who is sequencing what" and responsible researchers (contacts), funding sources, sequencing centers etc
      • +
    +
    • +
  • Genome browsers +
      +
    • Display features (genes, transcripts...) on the genomes, show annotations (conflicts, variants also included), homolog search
      • +
    • UCSC genome browser, Ensembl (popular in Europe)
      • +
    • Pros and cons of genome browsers +
        +
      • Pros +
          +
        • easy to use
          • +
        • regularly updated
          • +
        • automated annotation pipelines => fast to include new genomes
          • +
        • very powerful export utilities (BioMart in Ensembl)
          • +
        • API for local access
          • +
        • DAS (distributed annotation system) for data exchange
          • +
        • long term project, stable funding, likely not going away
          • +
        +
        • +
      • Cons +
          +
        • focus on vertebrates, few other genomes
          • +
        • complex db schema
          • +
        • popular, so can be slow
          • +
        +
        • +
      +
      • +
    +
    • +
+

Special ones:

+
    +
  • Comparative genomics databases +
      +
    • STRING (protein-protein interactions, focused on microbial genomes, maintained by von Mering group at UZH)
      • +
    • specialized on comparing genomes (at nucleotide-level, or gene-level)
      • +
    • to visualize evidence of selection (exons, regulatory sites, ...)
      • +
    • to infer past evolution of genomes (rearrangements, gains, losses, ...)
      • +
    • to establish gene histories (orthology, paralogy, synteny, ...)
      • +
    • often require extensive offline computation before they go online
      • +
    • some of their services also offered by generic genome browsers/sites.
      • +
    +
    • +
  • Organism-specific databases +
      +
    • Flybase, Wormbase, TAIR, SGD...
      • +
    • community driven, extensive manual input
      • +
    • specific terms, abbreviations, gene names...
      • +
    +
    • +
  • Specialized databases +
      +
    • IGSR: human population genetics
      • +
    • OMIM: known disease-causing mutations
      • +
    • KEGG: metabolic pathways and enzymes
      • +
    +
    • +
+
+

Modern Genomics II

+

I cannot understand his accent...

+ +

Contents that (I think) are important

+

Linkage disequilibrium (LD)

+

Coefficient of linkage disequilibrium \( D \)

+

Given two loci \(A\) and \(B\) (can have allele \(A\) or \(a\), \(B\) or \(b\)), the coefficient of linkage disequilibrium \(D\) is defined as

+

\[ +D = \frac{P_{AB} - P_A P_B}{P_A P_B} +\]

+

Below shows two examples of \(D\) calculation.

+

LD example 1

+

\[ +D = \frac{P_{AB} - P_{A} P_{B}}{P_{A} P_{B}} = \frac{5}{12} - \frac{8}{12}\times\frac{6}{12} = \frac{1}{12} +\]

+

A and B are linked to some extent.

+

LD example 2

+

\[ +D = \frac{P_{AB} - P_{A} P_{B}}{P_{A} P_{B}} = \frac{6}{12} - \frac{8}{12}\times\frac{9}{12} = 0 +\]

+

Here A and B are not linked at all.

+

Basically we are testing whether P(A) and P(B) are independent.

+

Relative measures of LD

+
    +
  1. \(r^2 = \frac{D}{P_A P_a P_B P_b}\)
    2. +
  2. \(D' = \frac{D}{D_{\max}}\) if \(D\) is positive, \(D' = \frac{D}{D_{\min}}\) if \(D\) is negative
    3. +
+

Nucleotide diversity \(\pi\)

+

Average proportion of pairwise differences between the sequences

+

Give a multiple sequence alignment, \(\pi\) is defined as

+

\[ +\pi = \sum_{i < j} \frac{\pi_{ij}}{n_c} +\]

+

where \(n_c = \frac{n(n-1)}{2}\) is the number of pairwise comparisons, and \(\pi_{ij}\) is the proportion of differences between the \(i\)th and \(j\)th sequences.

+

Below shows an example of \(\pi\) calculation.

+

Nucleotide diversity example

+

\[ +\pi = \sum_{i < j} \frac{\pi_{ij}}{n_c} = \frac{\pi_{12} + \pi_{13} + \pi_{23}}{3} = 0.2 +\]

+

Basically just calculating the average number of differences in the matrix.

+

Course contents according to recording

+

Title: Applications of next-generation sequencing and other genomic techniques

+
    +
  1. Resequencing to identify genetic basis of phenotypic variation +
      +
    1. Outlier approach
      2. +
    2. Genome-wide association studies (GWAS) and linkage disequilibrium
      3. +
    +
    2. +
  2. Introduction to RNA-seq (transcriptome) focusing on genome duplication
    3. +
  3. Resequencing to detect signature of selection: nucleotide diversity
    4. +
+

Microbial community and metagenomics, ChIP-seq, epigenomics, whole genome assembly as reference

+
    +
  • Evolutionary functional genomics can... +
      +
    • identify ecologically relevant genes
      • +
    • inferring selection & population processes
      • +
    +
    • +
+

Transcriptomics I

+

Unimportant text is grayed out but worth reading for fluency and context.

+ +

Motivation

+

We are interested in the expression of genes in a +cell. Altough proteins are the actors of genes instead of mRNA +transcripts, mRNAs transcripts are easier to measure because selection +has chosen them to convey the genetic message in a faithful way. Also there are +plenty of interesting non-coding RNAs.

+

RNA species

+

80% of the total RNA is rRNA. 14% is tRNA. Only 1-3% is mRNA. All other species +account for the remaining 1-3%.

+

RNA speciesPrevalence of RNA species

+

RNA selection methods

+

RNA selection methods

+
    +
  • A: total RNA +
      +
    • Unbiased estimation
      • +
    • Dominate by rRNA, not very informative
      • +
    +
    • +
  • B: ribosomal reduction/depletion +
      +
    • Use probes that bind to rRNA and pull them out
      • +
    • < 5% rRNA left
      • +
    +
    • +
  • C: poly-A selection +
      +
    • Use probes that bind to poly-A tails
      • +
    • Selects for mRNA, and also some long non-coding RNAs (because they also have +poly-A tails)
      • +
    +
    • +
  • D: cDNA capture +
      +
    • Design target probes that bind to a certain set of RNAs
      • +
    • Limited transcriptome coverage
      • +
    +
    • +
+

90% of transcriptome research utilize poly-A +selection; 5% of them go for ribosomal depletion because their mRNAs are of low +quality and fragmented. The rest 5% do have high-quality mRNAs but still go for +ribosomal depletion because they want to estimate other RNA species at the same +time.

+

Note: current illumina sequencers cannot sequence miRNAs (20-25nt) and mRNA +fragments (100-300nt) together (because of the large length discrepency)

+

RNA-seq experiment workflow overview

+

A typical RNA-seq experiment workflow is shown below.

+

Typical RNA-seq experiment

+

We can do either single-read sequencing or paired-end +sequencing (as is shown in the figure above) in the third step.

+

Paired-end sequencing

+

It can also be summarized into a flow diagram.

+

RNA-seq workflow diagram

+

The following sections will go into more details about each step.

+

RNA-seq experiment design

+
    +
  • RNA-seq experiments are implemented as comparative experiments
    • +
  • RNA-seq is used to measure the relative abundance (expression) of each +mRNA (gene) in a sample +
      +
    • sample: We +cannot sequence all the RNA fragments. Instead, we randomly select about 20M +fragments as a representation of the total RNA obtained. Note that we can +sample multiple times.
      • +
    +
    • +
  • RNA-seq can link gene expression to +
      +
    • genotype
      • +
    • phenotype
      • +
    • treatment response
      • +
    +
    • +
+

RNA-seq read mapping methods

+

Considerations

+

Ideally, the read mapping process is as simple as +sequencing the transcribed RNAs and then mapping the +sequences back to the genome to identify the gene expression.

+

However, in reality, the process is much more +complicated because current sequencers can only perform faithful sequencing +up to a couple of hundreds of bp (usually 200-800bp), and a typical mRNA is +2-3kb long. Thus, the mRNA needs to be first chopped into fragments and then +sequenced. When we do the mapping, we're mapping the chopped reads back to the +genome instead of the whole spliced sequences. The existence of alternative +splicing (protein isoforms) and sequencing errors makes the mapping +process even more complicated.

+

While discussing the mapping process, those +limitations and problems should be kept in mind.

+

How to map reads to a genome?

+
    +
  • Mapping algorithms must be +
      +
    • Fast +
        +
      • Thus usually find perfect or near-perfect (tolerating 1bp mismatch) match
        • +
      +
      • +
    • Able to handle SNPs, indels and sequencing errors
      • +
    +
    • +
+

We can always perform sequence alignment (here needs local +alignment/Smith-Waterman alignment). Of course the score matrix should be +good to determine the correct alignment. But this is slow because it requires +quadratic efforts.

+

What if we want to map billions of reads?

+
    +
  • Indexing method +
      +
    • Reads are aligned by index lookup instead of $O(n^2)$ seq comparison
      • +
    • Usually hashed so the lookup time is much faster
      • +
    • If lookup fails, actual sequence comparison is performed (more details on +this in next chapter)
      • +
    • Major aligners use the Burrows-Wheeler transform (BWT) to index +the reference genome +
        +
      • Very small. Even for the human genome the index +fits into 3GB RAM.
        • +
      +
      • +
    +
    • +
  • Example aligners + +
    • +
+

How to deal with SNPs and indels?

+
    +
  • SNPs +
      +
    • Can always be handled by performing real +Smith-Waterman alignment but expensive
      • +
    • At mismatched positions, try all possible bases and search the BWT index +again +
        +
      • Computing effort grows exponentially
        • +
      +
      • +
    • Gapped alignment +
        +
      • Chop reads into short segments (seeds)
        • +
      • align those seeds in a mismatch-free manner (typically using BWT +index lookup again)
        • +
      • stitch them back together
        • +
      • Might require multiple rounds of chopping
        • +
      +
      • +
    +
    • +
  • Indels +
      +
    • Can only be found with gapped alignment (described above), BWT lookup is +not enough
      • +
    +
    • +
+

How to deal with introns (basically very large insertions)?

+
    +
  • Approaches +
      +
    • Map directly to trapscript sequences (no intron) not to the genome +
        +
      • Pro: introns are not a problem
        • +
      • Cons: unknown genes/isoforms cannot be detected
        • +
      +
      • +
    • Spliced alignment to genome +
        +
      • Pro: finds reads from unknown gene loci or unknown isoforms
        • +
      • Con: larger search space, potentially more false positives, wrong +alignment to pseudogenes
        • +
      +
      • +
    • Combination of above
      • +
    +
    • +
  • Difference between spliced alignment and gapped alignment +
      +
    • Gapped alignment: longer gaps means high score penalty and lower score
      • +
    • Spliced alignment: long gaps at canonical splice-sites are allowed, +but lacking canonical splice-sites or gaps elsewhere (at non-canonical +splice sites) are penalized
      • +
    +
    • +
  • Pseudogenes +
      +
    • associated retrotransposed spliced sequence of a certain gene, thus +intron-free, and appears "exonic"
      • +
    • Have almost the same sequence as the original gene
      • +
    • Not functional because they do not have access to promotors so won't be +transcribed
      • +
    • Usually contain more mutations because there are no selection pressures to +keep them intact
      • +
    • Exonic reads will map to both the gene and its pseudogene, but likely +preferring gene placement due to lack of mutations
      • +
    • A spliced read could be incorrectly assigned to the pseudogene as it appears +to be exonic, preventing higher scoring spliced alignments from being +pursued
      • +
    +
    • +
+

Bowtie

+

Bowtie

+
    +
  • Step-by-step backward searching the suffix of the query sequence in +the BWT index +
      +
    • Exact matching
      • +
    +
    • +
  • Searched suffix appears consecutively in BWT
    • +
  • The size of range in BWT shrinks or remains the same
    • +
  • almost does not handle mismatches; a single mismatch will lead to +empty BWT range / failed index lookup +
      +
    • mismatches can come from +
        +
      • Sequencing error (illumina: $1/1000$)
        • +
      • True variation (SNPs, human mutation rate $\approx 1/10^4$
        • +
      +
      • +
    • mismatches are not rare events! at least 10% of >100nt reads
      • +
    +
    • +
  • Empty BWT range activates backtracking +
      +
    • All possible bases are tried at the mismatched position
      • +
    • Gapped alignment
      • +
    +
    • +
+

TopHat2

+

Handles mismatches by gapped alignment. It first performs (optional) +transcriptome alignment (exonic), and then performs genome +alignment for the unmapped reads. The unmapped reads in the second step are +multi-exon spanning reads and undergo spliced alignment by chopping the +reads into even shorter segments and splice site identification etc.

+
+

The figure is too complicated, not recommended to go into details but still +attached here for reference. TopHat2 pipeline

+
+

STAR

+

Direct alignment of non-contiguous sequences to the reference genome.

+
    +
  • First find Maximal Mappable Prefix (MMP) of the read +
      +
    • MMP is the longest prefix of the read that can be mapped to the reference +genome
      • +
    • MMP is found by searching the BWT index
      • +
    • Possible to tolerate a certain degree of mismatches using extend mode
      • +
    +
    • +
  • Stop extending MMP if MMP covers the whole read or encounters a mismatch
    • +
  • In the second case, find the MMP of the remaining suffix of the read
    • +
  • Repeat until the whole read is covered +
      +
    • Possible to use trim mode to get rid of A-tail or adapter sequence
      • +
    +
    • +
+STAR +

Quality control and reporting considerations after mapping

+

PHREAD quality

+
    +
  • Each called base is given a quality score $Q$
    • +
  • $Q = -10 \log_{10}(p)$ (PHRED score) +
      +
    • $p$ is the estimated probability of the base being called incorrectly
      • +
    • $Q$ is the negative log of the probability +
        +
      • Q-score = 10: prob = 0.1
        • +
      • Q-score = 20: prob = 0.01
        • +
      • Q-score = 30: prob = 0.001
        • +
      +
      • +
    • Q30 is often used as a cutoff for high quality reads
      • +
    +
    • +
  • How to use: downweight the low-quality bases when computing the alignment +score
    • +
  • First introduced for capillary sequencers
    • +
  • PHRED scores are determined by the sequencer that +directly rates how reliable the measured signal is
    • +
+

Read trimming

+

Not all parts of the read are useful for alignment. It is common to trim the +reads.

+
    +
  • Reasons for trimming: +
      +
    • Systemetic errors of sequencer +
        +
      • Illumina sequencers have high error rate at the first few bases
        • +
      • Basically all sequencers have increasing error rate towards the end of the +read
        • +
      +
      • +
    • Adapter trimming +
        +
      • If the inserted DNA/RNA fragment is too short, the read will contain part +of the adapter (since the sequencer generally will sequence 100bp at each +end)
        • +
      • Can be challenging if: +
          +
        • The inserted sequence is 90-100bp -- the incorporated adapter sequence +will only be a few bp long
          • +
        • The read has many sequencing errors
          • +
        +
        • +
      +
      • +
    • 3'-bias / degradation +
        +
      • The 3' end of the read is generally more likely to be degraded than the 5' +end
        • +
      • Depending on RNA degradation and extration protocols reads may not be +equally distributed along the transcripts
        • +
      +
      • +
    +
    • +
  • Trimming methods +
      +
    • Hard trimming: trim a fixed number of bases from the beginning and/or +end
      • +
    • Quality trimming: cut the end of the read as soon as the base quality +drops below a threshold
      • +
    • Soft trimming: trim the read that cannot be aligned to the reference +genome
      • +
    +
    • +
+

Multiple alignments and report considerations

+
    +
  • A read may have multiple valid alignments with identical or similarly good +alignment scores +
      +
    • Aligners may use different reporting strategies: +
        +
      • Randomly select one alignment from the top-scoring alignments
        • +
      • Report all alignments that are within delta of the +top-scoring alignment; clip if more than $N_{max}$ alignments are found
        • +
      • Report only alignments if they are unique (no other alignment within +delta of the alignment score)
        • +
      • Do not report anything if more than $N_{max}$ valid alignments are found
        • +
      • …
        • +
      +
      • +
    +
    • +
  • Whether a read has a unique alignment depends on +
      +
    • the read sequence and the sequence homology of the organism
      • +
    • the search algorithm of the aligner
      • +
    +
    • +
  • Whether a read has a single reported alignment depends additionally on +
      +
    • the reporting options strategy of the aligner
      • +
    +
    • +
+

Expression quantification

+
    +
  • Expression quantification on +
      +
    • Gene level +
        +
      • Reads belong to a gene locus
        • +
      +
      • +
    • Isoform level +
        +
      • Reads belong to an isoform
        • +
      +
      • +
    +
    • +
+

How to count reads?

+
    +
  • Unique mapped reads +
      +
    • Multi-reads are ignored – potentially biased quantification
      • +
    +
    • +
  • All mapped reads +
      +
    • Assignment of multi-reads need abundance estimation of overlapped +genes/isoforms
      • +
    +
    • +
+

Read counting

+

EM estimation

+
    +
  • General steps +
      +
    1. Estimate abundances based on uniquely mapping reads only
      2. +
    2. For each multi-read, divide it between the transcripts to which it maps, proportionally to their abundances estimated in the first step
      3. +
    3. Recompute abundances based on updated counts for each transcript +r.
      4. +
    4. Continue with Step 2
      5. +
    +
    • +
  • Model the sequencing and analysis process with a likelihood function
    • +
  • E-step: Compute expected read counts given current expression levels
    • +
  • M-step: Compute expression values maximizing likelihood given expected read counts
    • +
+

Alignment-free RNA-seq quantification

+

Instead of building BWT, we build hashed k-mer index based on known +transcriptome, and search the k-mers in the reads to map and compute abundance.

+

Easier to understand through side-by-side comparison with the traditional +alignment dependent method:

+

Alignment dependent v.s. alignment free

+

While allocating k-mer to transcript, we try to make each transcript covered +as uniformly as possible.

+
    +
  • Pros +
      +
    • Accurate and fast in quantifying KNOWN TRANSCRIPTS
      • +
    • Counts can be aggregated to get gene-level quantification
      • +
    +
    • +
  • Cons +
      +
    • Less well annotated genomes – less accurate results
      • +
    • No alignments – no information about SNPs
      • +
    • Transcript coverage is not uniform
      • +
    +
    • +
+

Normalization

+

Transcriptomics II

+ + +

Methods of Exploratory Data Analysis

+

Typical shape of data we have in hand: a data matrix.

+

Data matrix

+

where the columns are the samples and the rows are the features (usually gene expressions). (It can be the other way around, but this is the most common case.)

+
    +
  • Clustering +
      +
    • Hierarchical clustering
      • +
    • k-means clustering
      • +
    +
    • +
  • Dimensionality reduction +
      +
    • Matrix Factorization +
        +
      • PCA
        • +
      • MDS (Multidimensional Scaling)
        • +
      +
      • +
    • Graph-based methods +
        +
      • t-SNE
        • +
      • UMAP
        • +
      +
      • +
    +
    • +
+

Clustering

+
    +
  • Goals +
      +
    • group similar samples +
        +
      • evaluate similarity between expression profiles of the samples
        • +
      • test if similarities match the experimental design and effect sizes
        • +
      • test if variations within condition is smaller than between conditions
        • +
      • outliers detection
        • +
      +
      • +
    • group similar genes +
        +
      • guilt by association: infer functions of unknown genes from known genes with the same expression pattern (co-expression)
        • +
      +
      • +
    +
    • +
+

Distance measures

+

To cluster samples, we need to first define a "distance" measure between samples.

+

Commonly used distance measures:

+
    +
  • Euclidean distance (typically for clustering samples) +
      +
    • Euclidean distance of two profiles $\mathbf{x}$ and $\mathbf{y}$ with $p$ genes (i.e. the distance between two $p$-dimensional vectors $\mathbf{x}$ and $\mathbf{y}$)
      • +
    • $d(\mathbf{x}, \mathbf{y}) = \sqrt{\sum_{i=1}^{p} \left(x_i - y_i\right)^2}$
      • +
    • Expression values MUST BE LOG SCALE
      • +
    +
    • +
  • $1 - \text{corr}(\mathbf{x}, \mathbf{y})$ (typically for clustering genes) +
      +
    • Correlation coefficient of two profiles $\mathbf{x}$ and $\mathbf{y}$ with $p$ samples
      • +
    • $\text{corr}(\mathbf{x}, \mathbf{y}) = \frac{\sum_{i=1}^{p}(x_i - \bar{x})(y_i - \bar{y})}{\sqrt{\sum_{i=1}^{p}(x_i - \bar{x})^2 \cdot \sum_{i-1}^{p}(y_i - \bar{y})^2}}$
      • +
    • $\bar{x} = \frac{1}{p}\sum_{i=1}^{p}x_i$
      • +
    • $\bar{y} = \frac{1}{p}\sum_{i=1}^{p}y_i$
      • +
    +
    • +
+

Hierarchical Clustering

+

Algorithm:

+
    +
  1. Compute the distance matrix ($n \times (n - 1) / 2 \rightarrow O(n^2)$) between all samples
    2. +
  2. Find pair with minimal distance and merge them
    3. +
  3. Update the distance matrix
    4. +
  4. Repeat 2-3 until all samples are merged
    5. +
+

Parameters:

+
    +
  • distance measure for samples +
      +
    • usually $1 - \text{corr}(\mathbf{x}, \mathbf{y})$ for gene expression
      • +
    +
    • +
  • distance measure for clusters (linkage rule) +
      +
    • Single linkage: minimum distance between any elements of the two clusters
      • +
    • Complete linkage: maximum distance between any elements of the two clusters
      • +
    • Average linkage: average distance between all elements of the two clusters
      • +
    • Ward's linkage: minimal increase in intra-cluster variance
      • +
    +
    • +
+

Input:

+
    +
  • distance matrix +
      +
    • The linkage can be derived directly from the distance matrix.
      • +
    • Hence clustering algorithm only needs the distrance matrix as input, not the measurements individually.
      • +
    +
    • +
+

k-means Clustering

+

Algorithm:

+
    +
  1. Randomly assign each sample to one of the $k$ clusters
    2. +
  2. Compute the centroid (cluster center, average of the assigned samples) of each cluster
    3. +
  3. Assign each sample to the cluster with the closest centroid
    4. +
  4. Repeat 2-3 until convergence or a maximum number of iterations
    5. +
+

Parameters:

+
    +
  • number of clusters $k$
    • +
  • distance measure for samples
    • +
+

Input:

+
    +
  • data matrix (cannot directly use distance matrix)
    • +
+

This method minimizes the intra-cluster variance.

+

Choice of $k$ affects the result.

+

Comparison of Hierarchical Clustering and k-means Clustering

+
+ + +
Hierarchical Clusteringk-means Clustering
Computing time$O(n^2 \log (n))$$O(n \cdot k \cdot t)$
  • $t$: number of iterations
  • $k$: number of clusters
Memory$O(n^2)$$O(n \cdot k)$
+
+

When clustering large numbers of genes (>1e4, hierarchical clustering is not practical

+

Dimensionality Reduction

+

Principal Component Analysis (PCA)

+

Goal: Find a new coordinate system such that the first axis (principal component) captures the most variance, the second axis captures the second most variance, and so on.

+

The data is linearly transformed to a new coordinate system.

+

t-SNE

+

Algorithm:

+
    +
  1. In the high-dimensional space, create a probability distribution that dictates how likely two points are to be neighbors.
    2. +
  2. Recreate a low dimensional space that follows the same probability distribution as best as possible.
    3. +
+

How to find the best low-dimensional representation:

+
    +
  • preserve the pairwise distances between neighboring points in the high-dimensional space
    • +
  • non-linear, different transformations on different regions
    • +
+

Characteristic:

+
    +
  • Powerful, but need to fiddle with random seed and perplexity
    • +
  • Non-deterministic
    • +
+

UMAP

+

Uniform Manifold Approximation and Projection

+

Approach: Find for each point the neighbors and build simplices (simplex: a generalization of the concept of a triangle or tetrahedron to arbitrary dimensions) and then optimize the low-dimensional representation to preserve the simplices.

+

Differential Expression Analysis

+ +
+ + +
+
+ + + +
+ + + + + + + + + + + + + + + + + + + + + +
+ + diff --git a/searcher.js b/searcher.js new file mode 100644 index 0000000..d2b0aee --- /dev/null +++ b/searcher.js @@ -0,0 +1,483 @@ +"use strict"; +window.search = window.search || {}; +(function search(search) { + // Search functionality + // + // You can use !hasFocus() to prevent keyhandling in your key + // event handlers while the user is typing their search. + + if (!Mark || !elasticlunr) { + return; + } + + //IE 11 Compatibility from https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/String/startsWith + if (!String.prototype.startsWith) { + String.prototype.startsWith = function(search, pos) { + return this.substr(!pos || pos < 0 ? 0 : +pos, search.length) === search; + }; + } + + var search_wrap = document.getElementById('search-wrapper'), + searchbar = document.getElementById('searchbar'), + searchbar_outer = document.getElementById('searchbar-outer'), + searchresults = document.getElementById('searchresults'), + searchresults_outer = document.getElementById('searchresults-outer'), + searchresults_header = document.getElementById('searchresults-header'), + searchicon = document.getElementById('search-toggle'), + content = document.getElementById('content'), + + searchindex = null, + doc_urls = [], + results_options = { + teaser_word_count: 30, + limit_results: 30, + }, + search_options = { + bool: "AND", + expand: true, + fields: { + title: {boost: 1}, + body: {boost: 1}, + breadcrumbs: {boost: 0} + } + }, + mark_exclude = [], + marker = new Mark(content), + current_searchterm = "", + URL_SEARCH_PARAM = 'search', + URL_MARK_PARAM = 'highlight', + teaser_count = 0, + + SEARCH_HOTKEY_KEYCODE = 83, + ESCAPE_KEYCODE = 27, + DOWN_KEYCODE = 40, + UP_KEYCODE = 38, + SELECT_KEYCODE = 13; + + function hasFocus() { + return searchbar === document.activeElement; + } + + function removeChildren(elem) { + while (elem.firstChild) { + elem.removeChild(elem.firstChild); + } + } + + // Helper to parse a url into its building blocks. + function parseURL(url) { + var a = document.createElement('a'); + a.href = url; + return { + source: url, + protocol: a.protocol.replace(':',''), + host: a.hostname, + port: a.port, + params: (function(){ + var ret = {}; + var seg = a.search.replace(/^\?/,'').split('&'); + var len = seg.length, i = 0, s; + for (;i': '>', + '"': '"', + "'": ''' + }; + var repl = function(c) { return MAP[c]; }; + return function(s) { + return s.replace(/[&<>'"]/g, repl); + }; + })(); + + function formatSearchMetric(count, searchterm) { + if (count == 1) { + return count + " search result for '" + searchterm + "':"; + } else if (count == 0) { + return "No search results for '" + searchterm + "'."; + } else { + return count + " search results for '" + searchterm + "':"; + } + } + + function formatSearchResult(result, searchterms) { + var teaser = makeTeaser(escapeHTML(result.doc.body), searchterms); + teaser_count++; + + // The ?URL_MARK_PARAM= parameter belongs inbetween the page and the #heading-anchor + var url = doc_urls[result.ref].split("#"); + if (url.length == 1) { // no anchor found + url.push(""); + } + + // encodeURIComponent escapes all chars that could allow an XSS except + // for '. Due to that we also manually replace ' with its url-encoded + // representation (%27). + var searchterms = encodeURIComponent(searchterms.join(" ")).replace(/\'/g, "%27"); + + return '' + result.doc.breadcrumbs + '' + + '' + + teaser + ''; + } + + function makeTeaser(body, searchterms) { + // The strategy is as follows: + // First, assign a value to each word in the document: + // Words that correspond to search terms (stemmer aware): 40 + // Normal words: 2 + // First word in a sentence: 8 + // Then use a sliding window with a constant number of words and count the + // sum of the values of the words within the window. Then use the window that got the + // maximum sum. If there are multiple maximas, then get the last one. + // Enclose the terms in . + var stemmed_searchterms = searchterms.map(function(w) { + return elasticlunr.stemmer(w.toLowerCase()); + }); + var searchterm_weight = 40; + var weighted = []; // contains elements of ["word", weight, index_in_document] + // split in sentences, then words + var sentences = body.toLowerCase().split('. '); + var index = 0; + var value = 0; + var searchterm_found = false; + for (var sentenceindex in sentences) { + var words = sentences[sentenceindex].split(' '); + value = 8; + for (var wordindex in words) { + var word = words[wordindex]; + if (word.length > 0) { + for (var searchtermindex in stemmed_searchterms) { + if (elasticlunr.stemmer(word).startsWith(stemmed_searchterms[searchtermindex])) { + value = searchterm_weight; + searchterm_found = true; + } + }; + weighted.push([word, value, index]); + value = 2; + } + index += word.length; + index += 1; // ' ' or '.' if last word in sentence + }; + index += 1; // because we split at a two-char boundary '. ' + }; + + if (weighted.length == 0) { + return body; + } + + var window_weight = []; + var window_size = Math.min(weighted.length, results_options.teaser_word_count); + + var cur_sum = 0; + for (var wordindex = 0; wordindex < window_size; wordindex++) { + cur_sum += weighted[wordindex][1]; + }; + window_weight.push(cur_sum); + for (var wordindex = 0; wordindex < weighted.length - window_size; wordindex++) { + cur_sum -= weighted[wordindex][1]; + cur_sum += weighted[wordindex + window_size][1]; + window_weight.push(cur_sum); + }; + + if (searchterm_found) { + var max_sum = 0; + var max_sum_window_index = 0; + // backwards + for (var i = window_weight.length - 1; i >= 0; i--) { + if (window_weight[i] > max_sum) { + max_sum = window_weight[i]; + max_sum_window_index = i; + } + }; + } else { + max_sum_window_index = 0; + } + + // add around searchterms + var teaser_split = []; + var index = weighted[max_sum_window_index][2]; + for (var i = max_sum_window_index; i < max_sum_window_index+window_size; i++) { + var word = weighted[i]; + if (index < word[2]) { + // missing text from index to start of `word` + teaser_split.push(body.substring(index, word[2])); + index = word[2]; + } + if (word[1] == searchterm_weight) { + teaser_split.push("") + } + index = word[2] + word[0].length; + teaser_split.push(body.substring(word[2], index)); + if (word[1] == searchterm_weight) { + teaser_split.push("") + } + }; + + return teaser_split.join(''); + } + + function init(config) { + results_options = config.results_options; + search_options = config.search_options; + searchbar_outer = config.searchbar_outer; + doc_urls = config.doc_urls; + searchindex = elasticlunr.Index.load(config.index); + + // Set up events + searchicon.addEventListener('click', function(e) { searchIconClickHandler(); }, false); + searchbar.addEventListener('keyup', function(e) { searchbarKeyUpHandler(); }, false); + document.addEventListener('keydown', function(e) { globalKeyHandler(e); }, false); + // If the user uses the browser buttons, do the same as if a reload happened + window.onpopstate = function(e) { doSearchOrMarkFromUrl(); }; + // Suppress "submit" events so the page doesn't reload when the user presses Enter + document.addEventListener('submit', function(e) { e.preventDefault(); }, false); + + // If reloaded, do the search or mark again, depending on the current url parameters + doSearchOrMarkFromUrl(); + } + + function unfocusSearchbar() { + // hacky, but just focusing a div only works once + var tmp = document.createElement('input'); + tmp.setAttribute('style', 'position: absolute; opacity: 0;'); + searchicon.appendChild(tmp); + tmp.focus(); + tmp.remove(); + } + + // On reload or browser history backwards/forwards events, parse the url and do search or mark + function doSearchOrMarkFromUrl() { + // Check current URL for search request + var url = parseURL(window.location.href); + if (url.params.hasOwnProperty(URL_SEARCH_PARAM) + && url.params[URL_SEARCH_PARAM] != "") { + showSearch(true); + searchbar.value = decodeURIComponent( + (url.params[URL_SEARCH_PARAM]+'').replace(/\+/g, '%20')); + searchbarKeyUpHandler(); // -> doSearch() + } else { + showSearch(false); + } + + if (url.params.hasOwnProperty(URL_MARK_PARAM)) { + var words = decodeURIComponent(url.params[URL_MARK_PARAM]).split(' '); + marker.mark(words, { + exclude: mark_exclude + }); + + var markers = document.querySelectorAll("mark"); + function hide() { + for (var i = 0; i < markers.length; i++) { + markers[i].classList.add("fade-out"); + window.setTimeout(function(e) { marker.unmark(); }, 300); + } + } + for (var i = 0; i < markers.length; i++) { + markers[i].addEventListener('click', hide); + } + } + } + + // Eventhandler for keyevents on `document` + function globalKeyHandler(e) { + if (e.altKey || e.ctrlKey || e.metaKey || e.shiftKey || e.target.type === 'textarea' || e.target.type === 'text') { return; } + + if (e.keyCode === ESCAPE_KEYCODE) { + e.preventDefault(); + searchbar.classList.remove("active"); + setSearchUrlParameters("", + (searchbar.value.trim() !== "") ? "push" : "replace"); + if (hasFocus()) { + unfocusSearchbar(); + } + showSearch(false); + marker.unmark(); + } else if (!hasFocus() && e.keyCode === SEARCH_HOTKEY_KEYCODE) { + e.preventDefault(); + showSearch(true); + window.scrollTo(0, 0); + searchbar.select(); + } else if (hasFocus() && e.keyCode === DOWN_KEYCODE) { + e.preventDefault(); + unfocusSearchbar(); + searchresults.firstElementChild.classList.add("focus"); + } else if (!hasFocus() && (e.keyCode === DOWN_KEYCODE + || e.keyCode === UP_KEYCODE + || e.keyCode === SELECT_KEYCODE)) { + // not `:focus` because browser does annoying scrolling + var focused = searchresults.querySelector("li.focus"); + if (!focused) return; + e.preventDefault(); + if (e.keyCode === DOWN_KEYCODE) { + var next = focused.nextElementSibling; + if (next) { + focused.classList.remove("focus"); + next.classList.add("focus"); + } + } else if (e.keyCode === UP_KEYCODE) { + focused.classList.remove("focus"); + var prev = focused.previousElementSibling; + if (prev) { + prev.classList.add("focus"); + } else { + searchbar.select(); + } + } else { // SELECT_KEYCODE + window.location.assign(focused.querySelector('a')); + } + } + } + + function showSearch(yes) { + if (yes) { + search_wrap.classList.remove('hidden'); + searchicon.setAttribute('aria-expanded', 'true'); + } else { + search_wrap.classList.add('hidden'); + searchicon.setAttribute('aria-expanded', 'false'); + var results = searchresults.children; + for (var i = 0; i < results.length; i++) { + results[i].classList.remove("focus"); + } + } + } + + function showResults(yes) { + if (yes) { + searchresults_outer.classList.remove('hidden'); + } else { + searchresults_outer.classList.add('hidden'); + } + } + + // Eventhandler for search icon + function searchIconClickHandler() { + if (search_wrap.classList.contains('hidden')) { + showSearch(true); + window.scrollTo(0, 0); + searchbar.select(); + } else { + showSearch(false); + } + } + + // Eventhandler for keyevents while the searchbar is focused + function searchbarKeyUpHandler() { + var searchterm = searchbar.value.trim(); + if (searchterm != "") { + searchbar.classList.add("active"); + doSearch(searchterm); + } else { + searchbar.classList.remove("active"); + showResults(false); + removeChildren(searchresults); + } + + setSearchUrlParameters(searchterm, "push_if_new_search_else_replace"); + + // Remove marks + marker.unmark(); + } + + // Update current url with ?URL_SEARCH_PARAM= parameter, remove ?URL_MARK_PARAM and #heading-anchor . + // `action` can be one of "push", "replace", "push_if_new_search_else_replace" + // and replaces or pushes a new browser history item. + // "push_if_new_search_else_replace" pushes if there is no `?URL_SEARCH_PARAM=abc` yet. + function setSearchUrlParameters(searchterm, action) { + var url = parseURL(window.location.href); + var first_search = ! url.params.hasOwnProperty(URL_SEARCH_PARAM); + if (searchterm != "" || action == "push_if_new_search_else_replace") { + url.params[URL_SEARCH_PARAM] = searchterm; + delete url.params[URL_MARK_PARAM]; + url.hash = ""; + } else { + delete url.params[URL_MARK_PARAM]; + delete url.params[URL_SEARCH_PARAM]; + } + // A new search will also add a new history item, so the user can go back + // to the page prior to searching. A updated search term will only replace + // the url. + if (action == "push" || (action == "push_if_new_search_else_replace" && first_search) ) { + history.pushState({}, document.title, renderURL(url)); + } else if (action == "replace" || (action == "push_if_new_search_else_replace" && !first_search) ) { + history.replaceState({}, document.title, renderURL(url)); + } + } + + function doSearch(searchterm) { + + // Don't search the same twice + if (current_searchterm == searchterm) { return; } + else { current_searchterm = searchterm; } + + if (searchindex == null) { return; } + + // Do the actual search + var results = searchindex.search(searchterm, search_options); + var resultcount = Math.min(results.length, results_options.limit_results); + + // Display search metrics + searchresults_header.innerText = formatSearchMetric(resultcount, searchterm); + + // Clear and insert results + var searchterms = searchterm.split(' '); + removeChildren(searchresults); + for(var i = 0; i < 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» Notes taken @ ETH Zurich","id":"0","title":"Notes taken @ ETH Zurich"},"1":{"body":"Here I list all courses I took at ETH Zurich and provide a brief overview of the course content. The clickable links will lead you to the respective course notes. Courses are organized by semester and year. The course notes are organized by lecture.","breadcrumbs":"Home » Introduction","id":"1","title":"Introduction"},"10":{"body":"Efficient sequencing technology arrived rather late. Initially the sequencing process was cumbersome and radioactive. 1975: \"dideoxy\" DNA sequencing (Sanger) 1977: first genome (bacteriophage \\( \\phi X 174 \\) ) 1995: first cell (Haemophilus influenzae) 1998: first animal (Caenorhabditis elegans) 2001: Homo sapiens Today (February 2023) genomes available for: 409,947 Bacteria, 4,988 Archaea, 47,200 Eukaryotes human genomes fairly routine below 1000$ raw costs \"Personal Genome Projects\" are enrolling 100’000s of volunteers, including their medical records","breadcrumbs":"Functional Genomics » Modern Genomics I » Timeline","id":"10","title":"Timeline"},"11":{"body":"Because we want an inventory of all genes and functions Because wea can compare genomes to learn about evolution, to get hints on gene function, etc Comparison can be either based on DNA or protein Alignments, dot plots, whole chromosome comparison","breadcrumbs":"Functional Genomics » Modern Genomics I » Why Genomics?","id":"11","title":"Why Genomics?"},"12":{"body":"Gene prediction Gene prediction algorithms that use homology (=comparative genomics result) information: SLAM, SGP, Twinscan (= N-SCAN)... UCSC genome browser gene prediction Gene family evolution","breadcrumbs":"Functional Genomics » Modern Genomics I » Comparative genomics use case examples","id":"12","title":"Comparative genomics use case examples"},"13":{"body":"","breadcrumbs":"Functional Genomics » Modern Genomics I » Classical sequencing method","id":"13","title":"Classical sequencing method"},"14":{"body":"Natural DNA extension requires 3'-OH. The dideoxy method uses a 2',3'-dideoxy nucleotide, which lacks the 3'-OH group. This causes the DNA chain to terminate. By introducing different dideoxy nucleotides, the sequence can be read.","breadcrumbs":"Functional Genomics » Modern Genomics I » Sanger (double-deoxy) sequencing","id":"14","title":"Sanger (double-deoxy) sequencing"},"15":{"body":"Variants of Sanger sequencing. Still utilize the dideoxy method to terminate DNA elongation. The difference is that the dideoxy nucleotides are labeled with different fluorescent dyes. The sequence is read by a laser. Two variants of Automated Dye Sequencing Dye terminator sequencing is now widely used over the rather cumbersome (4 tubes per sample) dye primer chemistry.","breadcrumbs":"Functional Genomics » Modern Genomics I » Automated Dye Sequencing","id":"15","title":"Automated Dye Sequencing"},"16":{"body":"Generally involves first amplifying the DNA, then sequencing it. Sequencing is done by detecting the nucleotides as they are incorporated into the growing DNA strand (sequencing by synthesis). High-throughput is achieved by parallelizing the sequencing process.","breadcrumbs":"Functional Genomics » Modern Genomics I » New (Next-generation) sequencing technologies","id":"16","title":"New (Next-generation) sequencing technologies"},"17":{"body":"First-generation amplification technology: needs DNA-library in bacterial vectors --> cumbersome and biased Improvement: get rid of bacteria Emulsion PCR Improvement: bacterium free, but still needs cloning %%{init: {\"graph\": {\"htmlLabels\": false}} }%%\ngraph TD A[\"`**Fragment** the DNA, ligate **adapters** to ends, make **single-stranded**`\"] --> B[\"Attach to microbeads\"] B --> C[\"`PCR-amplify, in a **water-oil emulsion**`\"] C --> D[\"`Enrich beads having successful amplifications, then place into regular lattice (see figure below for details)`\"] Emulsion PCR enrichment step In short, the enrichment is done by capturing the second (5'-end) primer of the PCR product onto a large polysyrene bead. PCR on solid support PCR on solid support","breadcrumbs":"Functional Genomics » Modern Genomics I » Amplification technologies","id":"17","title":"Amplification technologies"},"18":{"body":"Barcoding 10X technology","breadcrumbs":"Functional Genomics » Modern Genomics I » Barcoding and \"linked reads\"","id":"18","title":"Barcoding and \"linked reads\""},"19":{"body":"First-generation sequencing needs DNA size-separation on a gel Improvement: get rid of gel (sequencing by synthesis) Pyrosequencing Pyrosequencing Reversible terminator sequencing Reversible terminator sequencing Sequencing by semi-conductor Directly detects the release of H+ ions when a nucleotide is incorporated into the growing DNA strand. Sequencing by semi-conductor","breadcrumbs":"Functional Genomics » Modern Genomics I » Sequencing technologies","id":"19","title":"Sequencing technologies"},"2":{"body":"Computational Biology Data Mining I Information Systems for Engineers Computational Systems Biology","breadcrumbs":"Home » 22HS","id":"2","title":"22HS"},"20":{"body":"Illumina Illumina NovaSeq 6000 PCR on solid support reversible terminator sequencing read length ca. 250bp 1e14 bp per run Ion Torrent / Life Techn. Inc Ion Gene Studio S5 PCR on beads sequencing by semi-conductor read length ca. 600bp 1e10 bp per run","breadcrumbs":"Functional Genomics » Modern Genomics I » Current implementations of NGS","id":"20","title":"Current implementations of NGS"},"21":{"body":"Single molecule sequencing . No need for amplification . Characterized by extremely long reads, but also high error rates. Pacific Biosciences SMRT (single molecule real time) sequencing pacbio1 pacbio1 Oxford Nanopore MinION oxford nanopore Self-note : minimap2 is a popular aligner for long reads.","breadcrumbs":"Functional Genomics » Modern Genomics I » Third-generation sequencing technologies","id":"21","title":"Third-generation sequencing technologies"},"22":{"body":"Traditional genome sequencing requires individual cell isolation and cultivation . This is not possible for the majority of microorganisms. But one advantage is that it's possible to re-assemble the genome from the reads. Environmental sequencing: directly sequence DNA extracted from the environment without purification and clonal cultivation. Genome assembly is generally not possible. Self-note : data generated from environmental sequencing is typically large in size, but highly fragmented and contaminated. Lots of exciting research in this area.","breadcrumbs":"Functional Genomics » Modern Genomics I » Environmental sequencing","id":"22","title":"Environmental sequencing"},"23":{"body":"Novel gene discovery Sequence identity comparison to known genes But > 50% of the environmental genomes are not similar to any known genome Novel gene families Gene family clustering (similar samples have similar gene family distribution)","breadcrumbs":"Functional Genomics » Modern Genomics I » How to deal with environmental sequencing data","id":"23","title":"How to deal with environmental sequencing data"},"24":{"body":"","breadcrumbs":"Functional Genomics » Modern Genomics I » Single-cell sequencing","id":"24","title":"Single-cell sequencing"},"25":{"body":"Heterogeneity in cell populations Tumor cells Immune cells Microbial communities Developmental biology","breadcrumbs":"Functional Genomics » Modern Genomics I » Why?","id":"25","title":"Why?"},"26":{"body":"In short, we first get single cells, then amplify the whole genome and sequence it. The challenges lie in the bolded parts. Single-cell isolation (In the very first \"single cell\" genomics paper, the \"single\" cells were literally picked manually...nowadays we don't do that) Sorting with optical tweezers Optic tweezers Dilution series Flow sorting Flow sorting Whole genome amplification Steps summarized: MDA phi 29 debranching S1 nuclease digestion DNA pol I nick translation Cloning Isothermal Multiple displacement amplification (MDA) Phi29 DNA polymerase Random primers Isothermal amplification MDA After MDA, we obtained a \" hyperbranched chromosome \". After debranching and cloning, we can sequence and re-assemble the genome. Next steps The debranching is done by incubating phi 29 DNA pol with hyperbranched DNA without any primer . The strand-replacement activity of phi 29 DNA pol will remove the hyperbranched structure. S1 nucleases are used to remove the remaining single-stranded DNA. Nicks are filled in by DNA pol I (has 5'->3' exonuclease activity).","breadcrumbs":"Functional Genomics » Modern Genomics I » How?","id":"26","title":"How?"},"27":{"body":"This section likely won't be covered in the exam. General popular resources : Raw data: NCBI sequence read archive (SRA) (also it's European counterpart, EBI European Nucleotide Archive (ENA) , but they are basically the same thing now) seq quality score included but incomplete: legacy & newer data not available gigantic in size Sequencing projects: GOLD (Genomes OnLine Database) keep track of \"who is sequencing what\" and responsible researchers (contacts), funding sources, sequencing centers etc Genome browsers Display features (genes, transcripts...) on the genomes, show annotations (conflicts, variants also included), homolog search UCSC genome browser, Ensembl (popular in Europe) Pros and cons of genome browsers Pros easy to use regularly updated automated annotation pipelines => fast to include new genomes very powerful export utilities (BioMart in Ensembl) API for local access DAS (distributed annotation system) for data exchange long term project, stable funding, likely not going away Cons focus on vertebrates, few other genomes complex db schema popular, so can be slow Special ones: Comparative genomics databases STRING (protein-protein interactions, focused on microbial genomes, maintained by von Mering group at UZH) specialized on comparing genomes (at nucleotide-level, or gene-level) to visualize evidence of selection (exons, regulatory sites, ...) to infer past evolution of genomes (rearrangements, gains, losses, ...) to establish gene histories (orthology, paralogy, synteny, ...) often require extensive offline computation before they go online some of their services also offered by generic genome browsers/sites. Organism-specific databases Flybase, Wormbase, TAIR, SGD... community driven, extensive manual input specific terms, abbreviations, gene names... Specialized databases IGSR: human population genetics OMIM: known disease-causing mutations KEGG: metabolic pathways and enzymes","breadcrumbs":"Functional Genomics » Modern Genomics I » Genomic databases","id":"27","title":"Genomic databases"},"28":{"body":"I cannot understand his accent... Contents that (I think) are important Linkage disequilibrium (LD) Coefficient of linkage disequilibrium ( D ) Relative measures of LD Nucleotide diversity (\\pi) Course contents according to recording","breadcrumbs":"Functional Genomics » Modern Genomics II » Modern Genomics II","id":"28","title":"Modern Genomics II"},"29":{"body":"","breadcrumbs":"Functional Genomics » Modern Genomics II » Contents that (I think) are important","id":"29","title":"Contents that (I think) are important"},"3":{"body":"Mobile Health and Activity Monitoring Functional Genomics Introduction to Machine Learning Big Data for Engineers Statistical Models in Computational Biology No courses (except for seminar) taken in 23HS since I was doing an internship at Roche.","breadcrumbs":"Home » 23FS + HS","id":"3","title":"23FS + HS"},"30":{"body":"Coefficient of linkage disequilibrium \\( D \\) Given two loci \\(A\\) and \\(B\\) (can have allele \\(A\\) or \\(a\\), \\(B\\) or \\(b\\)), the coefficient of linkage disequilibrium \\(D\\) is defined as \\[ D = \\frac{P_{AB} - P_A P_B}{P_A P_B} \\] Below shows two examples of \\(D\\) calculation. LD example 1 \\[ D = \\frac{P_{AB} - P_{A} P_{B}}{P_{A} P_{B}} = \\frac{5}{12} - \\frac{8}{12}\\times\\frac{6}{12} = \\frac{1}{12} \\] A and B are linked to some extent. LD example 2 \\[ D = \\frac{P_{AB} - P_{A} P_{B}}{P_{A} P_{B}} = \\frac{6}{12} - \\frac{8}{12}\\times\\frac{9}{12} = 0 \\] Here A and B are not linked at all. Basically we are testing whether P(A) and P(B) are independent.","breadcrumbs":"Functional Genomics » Modern Genomics II » Linkage disequilibrium (LD)","id":"30","title":"Linkage disequilibrium (LD)"},"31":{"body":"\\(r^2 = \\frac{D}{P_A P_a P_B P_b}\\) \\(D' = \\frac{D}{D_{\\max}}\\) if \\(D\\) is positive, \\(D' = \\frac{D}{D_{\\min}}\\) if \\(D\\) is negative","breadcrumbs":"Functional Genomics » Modern Genomics II » Relative measures of LD","id":"31","title":"Relative measures of LD"},"32":{"body":"Average proportion of pairwise differences between the sequences Give a multiple sequence alignment, \\(\\pi\\) is defined as \\[ \\pi = \\sum_{i < j} \\frac{\\pi_{ij}}{n_c} \\] where \\(n_c = \\frac{n(n-1)}{2}\\) is the number of pairwise comparisons, and \\(\\pi_{ij}\\) is the proportion of differences between the \\(i\\)th and \\(j\\)th sequences. Below shows an example of \\(\\pi\\) calculation. Nucleotide diversity example \\[ \\pi = \\sum_{i < j} \\frac{\\pi_{ij}}{n_c} = \\frac{\\pi_{12} + \\pi_{13} + \\pi_{23}}{3} = 0.2 \\] Basically just calculating the average number of differences in the matrix.","breadcrumbs":"Functional Genomics » Modern Genomics II » Nucleotide diversity \\(\\pi\\)","id":"32","title":"Nucleotide diversity \\(\\pi\\)"},"33":{"body":"Title: Applications of next-generation sequencing and other genomic techniques Resequencing to identify genetic basis of phenotypic variation Outlier approach Genome-wide association studies ( GWAS ) and linkage disequilibrium Introduction to RNA-seq (transcriptome) focusing on genome duplication Resequencing to detect signature of selection: nucleotide diversity Microbial community and metagenomics, ChIP-seq, epigenomics, whole genome assembly as reference Evolutionary functional genomics can... identify ecologically relevant genes inferring selection & population processes","breadcrumbs":"Functional Genomics » Modern Genomics II » Course contents according to recording","id":"33","title":"Course contents according to recording"},"34":{"body":"Unimportant text is grayed out but worth reading for fluency and context. Motivation RNA species RNA selection methods RNA-seq experiment workflow overview RNA-seq experiment design RNA-seq read mapping methods Considerations How to map reads to a genome? What if we want to map billions of reads? How to deal with SNPs and indels? How to deal with introns (basically very large insertions)? Bowtie TopHat2 STAR Quality control and reporting considerations after mapping PHREAD quality Read trimming Multiple alignments and report considerations Expression quantification How to count reads? EM estimation Alignment-free RNA-seq quantification Normalization","breadcrumbs":"Functional Genomics » Transcriptomics I » Transcriptomics I","id":"34","title":"Transcriptomics I"},"35":{"body":"We are interested in the expression of genes in a cell. Altough proteins are the actors of genes instead of mRNA transcripts, mRNAs transcripts are easier to measure because selection has chosen them to convey the genetic message in a faithful way. Also there are plenty of interesting non-coding RNAs.","breadcrumbs":"Functional Genomics » Transcriptomics I » Motivation","id":"35","title":"Motivation"},"36":{"body":"80% of the total RNA is rRNA. 14% is tRNA. Only 1-3% is mRNA. All other species account for the remaining 1-3%.","breadcrumbs":"Functional Genomics » Transcriptomics I » RNA species","id":"36","title":"RNA species"},"37":{"body":"RNA selection methods A: total RNA Unbiased estimation Dominate by rRNA, not very informative B: ribosomal reduction/depletion Use probes that bind to rRNA and pull them out < 5% rRNA left C: poly-A selection Use probes that bind to poly-A tails Selects for mRNA, and also some long non-coding RNAs (because they also have poly-A tails) D: cDNA capture Design target probes that bind to a certain set of RNAs Limited transcriptome coverage 90% of transcriptome research utilize poly-A selection; 5% of them go for ribosomal depletion because their mRNAs are of low quality and fragmented. The rest 5% do have high-quality mRNAs but still go for ribosomal depletion because they want to estimate other RNA species at the same time. Note: current illumina sequencers cannot sequence miRNAs (20-25nt) and mRNA fragments (100-300nt) together (because of the large length discrepency)","breadcrumbs":"Functional Genomics » Transcriptomics I » RNA selection methods","id":"37","title":"RNA selection methods"},"38":{"body":"A typical RNA-seq experiment workflow is shown below. Typical RNA-seq experiment We can do either single-read sequencing or paired-end sequencing (as is shown in the figure above) in the third step. It can also be summarized into a flow diagram. The following sections will go into more details about each step.","breadcrumbs":"Functional Genomics » Transcriptomics I » RNA-seq experiment workflow overview","id":"38","title":"RNA-seq experiment workflow overview"},"39":{"body":"RNA-seq experiments are implemented as comparative experiments RNA-seq is used to measure the relative abundance (expression) of each mRNA (gene) in a sample sample: We cannot sequence all the RNA fragments. Instead, we randomly select about 20M fragments as a representation of the total RNA obtained. Note that we can sample multiple times. RNA-seq can link gene expression to genotype phenotype treatment response","breadcrumbs":"Functional Genomics » Transcriptomics I » RNA-seq experiment design","id":"39","title":"RNA-seq experiment design"},"4":{"body":"Biofluiddynamics Synthetic Biology I","breadcrumbs":"Home » 24FS","id":"4","title":"24FS"},"40":{"body":"","breadcrumbs":"Functional Genomics » Transcriptomics I » RNA-seq read mapping methods","id":"40","title":"RNA-seq read mapping methods"},"41":{"body":"Ideally, the read mapping process is as simple as sequencing the transcribed RNAs and then mapping the sequences back to the genome to identify the gene expression. However, in reality, the process is much more complicated because current sequencers can only perform faithful sequencing up to a couple of hundreds of bp (usually 200-800bp), and a typical mRNA is 2-3kb long. Thus, the mRNA needs to be first chopped into fragments and then sequenced. When we do the mapping, we're mapping the chopped reads back to the genome instead of the whole spliced sequences. The existence of alternative splicing (protein isoforms) and sequencing errors makes the mapping process even more complicated. While discussing the mapping process, those limitations and problems should be kept in mind. How to map reads to a genome? Mapping algorithms must be Fast Thus usually find perfect or near-perfect (tolerating 1bp mismatch) match Able to handle SNPs, indels and sequencing errors We can always perform sequence alignment (here needs local alignment/ Smith-Waterman alignment ). Of course the score matrix should be good to determine the correct alignment. But this is slow because it requires quadratic efforts. What if we want to map billions of reads? Indexing method Reads are aligned by index lookup instead of $O(n^2)$ seq comparison Usually hashed so the lookup time is much faster If lookup fails, actual sequence comparison is performed (more details on this in next chapter) Major aligners use the Burrows-Wheeler transform (BWT) to index the reference genome Very small. Even for the human genome the index fits into 3GB RAM. Example aligners bowtie , bowtie2 BWA TopHat2 STAR SOAP ... How to deal with SNPs and indels? SNPs Can always be handled by performing real Smith-Waterman alignment but expensive At mismatched positions, try all possible bases and search the BWT index again Computing effort grows exponentially Gapped alignment Chop reads into short segments (seeds) align those seeds in a mismatch-free manner (typically using BWT index lookup again) stitch them back together Might require multiple rounds of chopping Indels Can only be found with gapped alignment (described above), BWT lookup is not enough How to deal with introns (basically very large insertions)? Approaches Map directly to trapscript sequences (no intron) not to the genome Pro: introns are not a problem Cons: unknown genes/isoforms cannot be detected Spliced alignment to genome Pro: finds reads from unknown gene loci or unknown isoforms Con: larger search space, potentially more false positives, wrong alignment to pseudogenes Combination of above Difference between spliced alignment and gapped alignment Gapped alignment: longer gaps means high score penalty and lower score Spliced alignment: long gaps at canonical splice-sites are allowed, but lacking canonical splice-sites or gaps elsewhere (at non-canonical splice sites) are penalized Pseudogenes associated retrotransposed spliced sequence of a certain gene, thus intron-free , and appears \" exonic \" Have almost the same sequence as the original gene Not functional because they do not have access to promotors so won't be transcribed Usually contain more mutations because there are no selection pressures to keep them intact Exonic reads will map to both the gene and its pseudogene, but likely preferring gene placement due to lack of mutations A spliced read could be incorrectly assigned to the pseudogene as it appears to be exonic, preventing higher scoring spliced alignments from being pursued","breadcrumbs":"Functional Genomics » Transcriptomics I » Considerations","id":"41","title":"Considerations"},"42":{"body":"Bowtie Step-by-step backward searching the suffix of the query sequence in the BWT index Exact matching Searched suffix appears consecutively in BWT The size of range in BWT shrinks or remains the same almost does not handle mismatches ; a single mismatch will lead to empty BWT range / failed index lookup mismatches can come from Sequencing error (illumina: $1/1000$) True variation (SNPs, human mutation rate $\\approx 1/10^4$ mismatches are not rare events! at least 10% of >100nt reads Empty BWT range activates backtracking All possible bases are tried at the mismatched position Gapped alignment","breadcrumbs":"Functional Genomics » Transcriptomics I » Bowtie","id":"42","title":"Bowtie"},"43":{"body":"Handles mismatches by gapped alignment. It first performs (optional) transcriptome alignment (exonic), and then performs genome alignment for the unmapped reads. The unmapped reads in the second step are multi-exon spanning reads and undergo spliced alignment by chopping the reads into even shorter segments and splice site identification etc. The figure is too complicated, not recommended to go into details but still attached here for reference. TopHat2 pipeline","breadcrumbs":"Functional Genomics » Transcriptomics I » TopHat2","id":"43","title":"TopHat2"},"44":{"body":"Direct alignment of non-contiguous sequences to the reference genome. First find Maximal Mappable Prefix (MMP) of the read MMP is the longest prefix of the read that can be mapped to the reference genome MMP is found by searching the BWT index Possible to tolerate a certain degree of mismatches using extend mode Stop extending MMP if MMP covers the whole read or encounters a mismatch In the second case, find the MMP of the remaining suffix of the read Repeat until the whole read is covered Possible to use trim mode to get rid of A-tail or adapter sequence","breadcrumbs":"Functional Genomics » Transcriptomics I » STAR","id":"44","title":"STAR"},"45":{"body":"","breadcrumbs":"Functional Genomics » Transcriptomics I » Quality control and reporting considerations after mapping","id":"45","title":"Quality control and reporting considerations after mapping"},"46":{"body":"Each called base is given a quality score $Q$ $Q = -10 \\log_{10}(p)$ (PHRED score) $p$ is the estimated probability of the base being called incorrectly $Q$ is the negative log of the probability Q-score = 10: prob = 0.1 Q-score = 20: prob = 0.01 Q-score = 30: prob = 0.001 Q30 is often used as a cutoff for high quality reads How to use: downweight the low-quality bases when computing the alignment score First introduced for capillary sequencers PHRED scores are determined by the sequencer that directly rates how reliable the measured signal is","breadcrumbs":"Functional Genomics » Transcriptomics I » PHREAD quality","id":"46","title":"PHREAD quality"},"47":{"body":"Not all parts of the read are useful for alignment. It is common to trim the reads. Reasons for trimming: Systemetic errors of sequencer Illumina sequencers have high error rate at the first few bases Basically all sequencers have increasing error rate towards the end of the read Adapter trimming If the inserted DNA/RNA fragment is too short, the read will contain part of the adapter (since the sequencer generally will sequence 100bp at each end) Can be challenging if: The inserted sequence is 90-100bp -- the incorporated adapter sequence will only be a few bp long The read has many sequencing errors 3'-bias / degradation The 3' end of the read is generally more likely to be degraded than the 5' end Depending on RNA degradation and extration protocols reads may not be equally distributed along the transcripts Trimming methods Hard trimming : trim a fixed number of bases from the beginning and/or end Quality trimming : cut the end of the read as soon as the base quality drops below a threshold Soft trimming : trim the read that cannot be aligned to the reference genome","breadcrumbs":"Functional Genomics » Transcriptomics I » Read trimming","id":"47","title":"Read trimming"},"48":{"body":"A read may have multiple valid alignments with identical or similarly good alignment scores Aligners may use different reporting strategies: Randomly select one alignment from the top-scoring alignments Report all alignments that are within delta of the top-scoring alignment; clip if more than $N_{max}$ alignments are found Report only alignments if they are unique (no other alignment within delta of the alignment score) Do not report anything if more than $N_{max}$ valid alignments are found … Whether a read has a unique alignment depends on the read sequence and the sequence homology of the organism the search algorithm of the aligner Whether a read has a single reported alignment depends additionally on the reporting options strategy of the aligner","breadcrumbs":"Functional Genomics » Transcriptomics I » Multiple alignments and report considerations","id":"48","title":"Multiple alignments and report considerations"},"49":{"body":"Expression quantification on Gene level Reads belong to a gene locus Isoform level Reads belong to an isoform","breadcrumbs":"Functional Genomics » Transcriptomics I » Expression quantification","id":"49","title":"Expression quantification"},"5":{"body":"","breadcrumbs":"Mobile Health and Activity Monitoring » Mobile Health and Activity Monitoring","id":"5","title":"Mobile Health and Activity Monitoring"},"50":{"body":"Unique mapped reads Multi-reads are ignored – potentially biased quantification All mapped reads Assignment of multi-reads need abundance estimation of overlapped genes/isoforms Read counting EM estimation General steps Estimate abundances based on uniquely mapping reads only For each multi-read, divide it between the transcripts to which it maps, proportionally to their abundances estimated in the first step Recompute abundances based on updated counts for each transcript r. Continue with Step 2 Model the sequencing and analysis process with a likelihood function E-step: Compute expected read counts given current expression levels M-step: Compute expression values maximizing likelihood given expected read counts Alignment-free RNA-seq quantification Instead of building BWT, we build hashed k-mer index based on known transcriptome, and search the k-mers in the reads to map and compute abundance. Easier to understand through side-by-side comparison with the traditional alignment dependent method: Alignment dependent v.s. alignment free While allocating k-mer to transcript, we try to make each transcript covered as uniformly as possible. Pros Accurate and fast in quantifying KNOWN TRANSCRIPTS Counts can be aggregated to get gene-level quantification Cons Less well annotated genomes – less accurate results No alignments – no information about SNPs Transcript coverage is not uniform","breadcrumbs":"Functional Genomics » Transcriptomics I » How to count reads?","id":"50","title":"How to count reads?"},"51":{"body":"","breadcrumbs":"Functional Genomics » Transcriptomics I » Normalization","id":"51","title":"Normalization"},"52":{"body":"Methods of Exploratory Data Analysis Clustering Distance measures Hierarchical Clustering k-means Clustering Comparison of Hierarchical Clustering and k-means Clustering Dimensionality Reduction Principal Component Analysis (PCA) t-SNE UMAP Differential Expression Analysis","breadcrumbs":"Functional Genomics » Transcriptomics II » Transcriptomics II","id":"52","title":"Transcriptomics II"},"53":{"body":"Typical shape of data we have in hand: a data matrix. Data matrix where the columns are the samples and the rows are the features (usually gene expressions). (It can be the other way around, but this is the most common case.) Clustering Hierarchical clustering k-means clustering Dimensionality reduction Matrix Factorization PCA MDS (Multidimensional Scaling) Graph-based methods t-SNE UMAP","breadcrumbs":"Functional Genomics » Transcriptomics II » Methods of Exploratory Data Analysis","id":"53","title":"Methods of Exploratory Data Analysis"},"54":{"body":"Goals group similar samples evaluate similarity between expression profiles of the samples test if similarities match the experimental design and effect sizes test if variations within condition is smaller than between conditions outliers detection group similar genes guilt by association : infer functions of unknown genes from known genes with the same expression pattern (co-expression)","breadcrumbs":"Functional Genomics » Transcriptomics II » Clustering","id":"54","title":"Clustering"},"55":{"body":"To cluster samples, we need to first define a \"distance\" measure between samples. Commonly used distance measures: Euclidean distance (typically for clustering samples) Euclidean distance of two profiles $\\mathbf{x}$ and $\\mathbf{y}$ with $p$ genes (i.e. the distance between two $p$-dimensional vectors $\\mathbf{x}$ and $\\mathbf{y}$) $d(\\mathbf{x}, \\mathbf{y}) = \\sqrt{\\sum_{i=1}^{p} \\left(x_i - y_i\\right)^2}$ Expression values MUST BE LOG SCALE $1 - \\text{corr}(\\mathbf{x}, \\mathbf{y})$ (typically for clustering genes) Correlation coefficient of two profiles $\\mathbf{x}$ and $\\mathbf{y}$ with $p$ samples $\\text{corr}(\\mathbf{x}, \\mathbf{y}) = \\frac{\\sum_{i=1}^{p}(x_i - \\bar{x})(y_i - \\bar{y})}{\\sqrt{\\sum_{i=1}^{p}(x_i - \\bar{x})^2 \\cdot \\sum_{i-1}^{p}(y_i - \\bar{y})^2}}$ $\\bar{x} = \\frac{1}{p}\\sum_{i=1}^{p}x_i$ $\\bar{y} = \\frac{1}{p}\\sum_{i=1}^{p}y_i$","breadcrumbs":"Functional Genomics » Transcriptomics II » Distance measures","id":"55","title":"Distance measures"},"56":{"body":"Algorithm : Compute the distance matrix ($n \\times (n - 1) / 2 \\rightarrow O(n^2)$) between all samples Find pair with minimal distance and merge them Update the distance matrix Repeat 2-3 until all samples are merged Parameters : distance measure for samples usually $1 - \\text{corr}(\\mathbf{x}, \\mathbf{y})$ for gene expression distance measure for clusters ( linkage rule ) Single linkage: minimum distance between any elements of the two clusters Complete linkage: maximum distance between any elements of the two clusters Average linkage: average distance between all elements of the two clusters Ward's linkage: minimal increase in intra-cluster variance Input : distance matrix The linkage can be derived directly from the distance matrix. Hence clustering algorithm only needs the distrance matrix as input, not the measurements individually.","breadcrumbs":"Functional Genomics » Transcriptomics II » Hierarchical Clustering","id":"56","title":"Hierarchical Clustering"},"57":{"body":"Algorithm : Randomly assign each sample to one of the $k$ clusters Compute the centroid (cluster center, average of the assigned samples) of each cluster Assign each sample to the cluster with the closest centroid Repeat 2-3 until convergence or a maximum number of iterations Parameters : number of clusters $k$ distance measure for samples Input : data matrix (cannot directly use distance matrix) This method minimizes the intra-cluster variance . Choice of $k$ affects the result.","breadcrumbs":"Functional Genomics » Transcriptomics II » k-means Clustering","id":"57","title":"k-means Clustering"},"58":{"body":"Hierarchical Clustering k-means Clustering Computing time $O(n^2 \\log (n))$ $O(n \\cdot k \\cdot t)$ $t$: number of iterations$k$: number of clusters Memory $O(n^2)$ $O(n \\cdot k)$ When clustering large numbers of genes (>1e4, hierarchical clustering is not practical","breadcrumbs":"Functional Genomics » Transcriptomics II » Comparison of Hierarchical Clustering and k-means Clustering","id":"58","title":"Comparison of Hierarchical Clustering and k-means Clustering"},"59":{"body":"","breadcrumbs":"Functional Genomics » Transcriptomics II » Dimensionality Reduction","id":"59","title":"Dimensionality Reduction"},"6":{"body":"A course collectively taught by multiple professors. Multiple-choice exam, lots of memorization.","breadcrumbs":"Functional Genomics » Functional Genomics","id":"6","title":"Functional Genomics"},"60":{"body":"Goal : Find a new coordinate system such that the first axis (principal component) captures the most variance, the second axis captures the second most variance, and so on. The data is linearly transformed to a new coordinate system.","breadcrumbs":"Functional Genomics » Transcriptomics II » Principal Component Analysis (PCA)","id":"60","title":"Principal Component Analysis (PCA)"},"61":{"body":"Algorithm : In the high-dimensional space, create a probability distribution that dictates how likely two points are to be neighbors. Recreate a low dimensional space that follows the same probability distribution as best as possible. How to find the best low-dimensional representation: preserve the pairwise distances between neighboring points in the high-dimensional space non-linear, different transformations on different regions Characteristic: Powerful, but need to fiddle with random seed and perplexity Non-deterministic","breadcrumbs":"Functional Genomics » Transcriptomics II » t-SNE","id":"61","title":"t-SNE"},"62":{"body":"Uniform Manifold Approximation and Projection Approach: Find for each point the neighbors and build simplices (simplex: a generalization of the concept of a triangle or tetrahedron to arbitrary dimensions) and then optimize the low-dimensional representation to preserve the simplices.","breadcrumbs":"Functional Genomics » Transcriptomics II » UMAP","id":"62","title":"UMAP"},"63":{"body":"","breadcrumbs":"Functional Genomics » Transcriptomics II » Differential Expression Analysis","id":"63","title":"Differential Expression Analysis"},"7":{"body":"01. Modern Genomics I 02. Modern Genomics II 03. Transcriptomics I 04. Transcriptomics II 05. miRNAs and Other Small RNAs 06. Proteomics 07. Metabolomics 08. Single Cell Mass Cytometry 09. Protein Networks 10. Epigenomics and Gene Regulation 11. Quality Control and Standards","breadcrumbs":"Functional Genomics » Table of Contents","id":"7","title":"Table of Contents"},"8":{"body":"Introduction Timeline Why Genomics? Comparative genomics use case examples Classical sequencing method Sanger (double-deoxy) sequencing Automated Dye Sequencing New (Next-generation) sequencing technologies Amplification technologies Emulsion PCR PCR on solid support Barcoding and \"linked reads\" Sequencing technologies Pyrosequencing Reversible terminator sequencing Sequencing by semi-conductor Current implementations of NGS Third-generation sequencing technologies Environmental sequencing How to deal with environmental sequencing data Single-cell sequencing Why? How? Single-cell isolation Whole genome amplification Genomic databases","breadcrumbs":"Functional Genomics » Modern Genomics I » Modern Genomics I","id":"8","title":"Modern Genomics I"},"9":{"body":"Molecular biology is governed by the \"central dogma\". Genomics is basically studying the DNA part of it. 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» Notes taken @ ETH Zurich","id":"0","title":"Notes taken @ ETH Zurich"},"1":{"body":"Here I list all courses I took at ETH Zurich and provide a brief overview of the course content. The clickable links will lead you to the respective course notes. Courses are organized by semester and year. The course notes are organized by lecture.","breadcrumbs":"Home » Introduction","id":"1","title":"Introduction"},"10":{"body":"Efficient sequencing technology arrived rather late. Initially the sequencing process was cumbersome and radioactive. 1975: \"dideoxy\" DNA sequencing (Sanger) 1977: first genome (bacteriophage \\( \\phi X 174 \\) ) 1995: first cell (Haemophilus influenzae) 1998: first animal (Caenorhabditis elegans) 2001: Homo sapiens Today (February 2023) genomes available for: 409,947 Bacteria, 4,988 Archaea, 47,200 Eukaryotes human genomes fairly routine below 1000$ raw costs \"Personal Genome Projects\" are enrolling 100’000s of volunteers, including their medical records","breadcrumbs":"Functional Genomics » Modern Genomics I » Timeline","id":"10","title":"Timeline"},"11":{"body":"Because we want an inventory of all genes and functions Because wea can compare genomes to learn about evolution, to get hints on gene function, etc Comparison can be either based on DNA or protein Alignments, dot plots, whole chromosome comparison","breadcrumbs":"Functional Genomics » Modern Genomics I » Why Genomics?","id":"11","title":"Why Genomics?"},"12":{"body":"Gene prediction Gene prediction algorithms that use homology (=comparative genomics result) information: SLAM, SGP, Twinscan (= N-SCAN)... UCSC genome browser gene prediction Gene family evolution","breadcrumbs":"Functional Genomics » Modern Genomics I » Comparative genomics use case examples","id":"12","title":"Comparative genomics use case examples"},"13":{"body":"","breadcrumbs":"Functional Genomics » Modern Genomics I » Classical sequencing method","id":"13","title":"Classical sequencing method"},"14":{"body":"Natural DNA extension requires 3'-OH. The dideoxy method uses a 2',3'-dideoxy nucleotide, which lacks the 3'-OH group. This causes the DNA chain to terminate. By introducing different dideoxy nucleotides, the sequence can be read.","breadcrumbs":"Functional Genomics » Modern Genomics I » Sanger (double-deoxy) sequencing","id":"14","title":"Sanger (double-deoxy) sequencing"},"15":{"body":"Variants of Sanger sequencing. Still utilize the dideoxy method to terminate DNA elongation. The difference is that the dideoxy nucleotides are labeled with different fluorescent dyes. The sequence is read by a laser. Two variants of Automated Dye Sequencing Dye terminator sequencing is now widely used over the rather cumbersome (4 tubes per sample) dye primer chemistry.","breadcrumbs":"Functional Genomics » Modern Genomics I » Automated Dye Sequencing","id":"15","title":"Automated Dye Sequencing"},"16":{"body":"Generally involves first amplifying the DNA, then sequencing it. Sequencing is done by detecting the nucleotides as they are incorporated into the growing DNA strand (sequencing by synthesis). High-throughput is achieved by parallelizing the sequencing process.","breadcrumbs":"Functional Genomics » Modern Genomics I » New (Next-generation) sequencing technologies","id":"16","title":"New (Next-generation) sequencing technologies"},"17":{"body":"First-generation amplification technology: needs DNA-library in bacterial vectors --> cumbersome and biased Improvement: get rid of bacteria Emulsion PCR Improvement: bacterium free, but still needs cloning %%{init: {\"graph\": {\"htmlLabels\": false}} }%%\ngraph TD A[\"`**Fragment** the DNA, ligate **adapters** to ends, make **single-stranded**`\"] --> B[\"Attach to microbeads\"] B --> C[\"`PCR-amplify, in a **water-oil emulsion**`\"] C --> D[\"`Enrich beads having successful amplifications, then place into regular lattice (see figure below for details)`\"] Emulsion PCR enrichment step In short, the enrichment is done by capturing the second (5'-end) primer of the PCR product onto a large polysyrene bead. PCR on solid support PCR on solid support","breadcrumbs":"Functional Genomics » Modern Genomics I » Amplification technologies","id":"17","title":"Amplification technologies"},"18":{"body":"Barcoding 10X technology","breadcrumbs":"Functional Genomics » Modern Genomics I » Barcoding and \"linked reads\"","id":"18","title":"Barcoding and \"linked reads\""},"19":{"body":"First-generation sequencing needs DNA size-separation on a gel Improvement: get rid of gel (sequencing by synthesis) Pyrosequencing Pyrosequencing Reversible terminator sequencing Reversible terminator sequencing Sequencing by semi-conductor Directly detects the release of H+ ions when a nucleotide is incorporated into the growing DNA strand. Sequencing by semi-conductor","breadcrumbs":"Functional Genomics » Modern Genomics I » Sequencing technologies","id":"19","title":"Sequencing technologies"},"2":{"body":"Computational Biology Data Mining I Information Systems for Engineers Computational Systems Biology","breadcrumbs":"Home » 22HS","id":"2","title":"22HS"},"20":{"body":"Illumina Illumina NovaSeq 6000 PCR on solid support reversible terminator sequencing read length ca. 250bp 1e14 bp per run Ion Torrent / Life Techn. Inc Ion Gene Studio S5 PCR on beads sequencing by semi-conductor read length ca. 600bp 1e10 bp per run","breadcrumbs":"Functional Genomics » Modern Genomics I » Current implementations of NGS","id":"20","title":"Current implementations of NGS"},"21":{"body":"Single molecule sequencing . No need for amplification . Characterized by extremely long reads, but also high error rates. Pacific Biosciences SMRT (single molecule real time) sequencing pacbio1 pacbio1 Oxford Nanopore MinION oxford nanopore Self-note : minimap2 is a popular aligner for long reads.","breadcrumbs":"Functional Genomics » Modern Genomics I » Third-generation sequencing technologies","id":"21","title":"Third-generation sequencing technologies"},"22":{"body":"Traditional genome sequencing requires individual cell isolation and cultivation . This is not possible for the majority of microorganisms. But one advantage is that it's possible to re-assemble the genome from the reads. Environmental sequencing: directly sequence DNA extracted from the environment without purification and clonal cultivation. Genome assembly is generally not possible. Self-note : data generated from environmental sequencing is typically large in size, but highly fragmented and contaminated. Lots of exciting research in this area.","breadcrumbs":"Functional Genomics » Modern Genomics I » Environmental sequencing","id":"22","title":"Environmental sequencing"},"23":{"body":"Novel gene discovery Sequence identity comparison to known genes But > 50% of the environmental genomes are not similar to any known genome Novel gene families Gene family clustering (similar samples have similar gene family distribution)","breadcrumbs":"Functional Genomics » Modern Genomics I » How to deal with environmental sequencing data","id":"23","title":"How to deal with environmental sequencing data"},"24":{"body":"","breadcrumbs":"Functional Genomics » Modern Genomics I » Single-cell sequencing","id":"24","title":"Single-cell sequencing"},"25":{"body":"Heterogeneity in cell populations Tumor cells Immune cells Microbial communities Developmental biology","breadcrumbs":"Functional Genomics » Modern Genomics I » Why?","id":"25","title":"Why?"},"26":{"body":"In short, we first get single cells, then amplify the whole genome and sequence it. The challenges lie in the bolded parts. Single-cell isolation (In the very first \"single cell\" genomics paper, the \"single\" cells were literally picked manually...nowadays we don't do that) Sorting with optical tweezers Optic tweezers Dilution series Flow sorting Flow sorting Whole genome amplification Steps summarized: MDA phi 29 debranching S1 nuclease digestion DNA pol I nick translation Cloning Isothermal Multiple displacement amplification (MDA) Phi29 DNA polymerase Random primers Isothermal amplification MDA After MDA, we obtained a \" hyperbranched chromosome \". After debranching and cloning, we can sequence and re-assemble the genome. Next steps The debranching is done by incubating phi 29 DNA pol with hyperbranched DNA without any primer . The strand-replacement activity of phi 29 DNA pol will remove the hyperbranched structure. S1 nucleases are used to remove the remaining single-stranded DNA. Nicks are filled in by DNA pol I (has 5'->3' exonuclease activity).","breadcrumbs":"Functional Genomics » Modern Genomics I » How?","id":"26","title":"How?"},"27":{"body":"This section likely won't be covered in the exam. General popular resources : Raw data: NCBI sequence read archive (SRA) (also it's European counterpart, EBI European Nucleotide Archive (ENA) , but they are basically the same thing now) seq quality score included but incomplete: legacy & newer data not available gigantic in size Sequencing projects: GOLD (Genomes OnLine Database) keep track of \"who is sequencing what\" and responsible researchers (contacts), funding sources, sequencing centers etc Genome browsers Display features (genes, transcripts...) on the genomes, show annotations (conflicts, variants also included), homolog search UCSC genome browser, Ensembl (popular in Europe) Pros and cons of genome browsers Pros easy to use regularly updated automated annotation pipelines => fast to include new genomes very powerful export utilities (BioMart in Ensembl) API for local access DAS (distributed annotation system) for data exchange long term project, stable funding, likely not going away Cons focus on vertebrates, few other genomes complex db schema popular, so can be slow Special ones: Comparative genomics databases STRING (protein-protein interactions, focused on microbial genomes, maintained by von Mering group at UZH) specialized on comparing genomes (at nucleotide-level, or gene-level) to visualize evidence of selection (exons, regulatory sites, ...) to infer past evolution of genomes (rearrangements, gains, losses, ...) to establish gene histories (orthology, paralogy, synteny, ...) often require extensive offline computation before they go online some of their services also offered by generic genome browsers/sites. Organism-specific databases Flybase, Wormbase, TAIR, SGD... community driven, extensive manual input specific terms, abbreviations, gene names... Specialized databases IGSR: human population genetics OMIM: known disease-causing mutations KEGG: metabolic pathways and enzymes","breadcrumbs":"Functional Genomics » Modern Genomics I » Genomic databases","id":"27","title":"Genomic databases"},"28":{"body":"I cannot understand his accent... Contents that (I think) are important Linkage disequilibrium (LD) Coefficient of linkage disequilibrium ( D ) Relative measures of LD Nucleotide diversity (\\pi) Course contents according to recording","breadcrumbs":"Functional Genomics » Modern Genomics II » Modern Genomics II","id":"28","title":"Modern Genomics II"},"29":{"body":"","breadcrumbs":"Functional Genomics » Modern Genomics II » Contents that (I think) are important","id":"29","title":"Contents that (I think) are important"},"3":{"body":"Mobile Health and Activity Monitoring Functional Genomics Introduction to Machine Learning Big Data for Engineers Statistical Models in Computational Biology No courses (except for seminar) taken in 23HS since I was doing an internship at Roche.","breadcrumbs":"Home » 23FS + HS","id":"3","title":"23FS + HS"},"30":{"body":"Coefficient of linkage disequilibrium \\( D \\) Given two loci \\(A\\) and \\(B\\) (can have allele \\(A\\) or \\(a\\), \\(B\\) or \\(b\\)), the coefficient of linkage disequilibrium \\(D\\) is defined as \\[ D = \\frac{P_{AB} - P_A P_B}{P_A P_B} \\] Below shows two examples of \\(D\\) calculation. LD example 1 \\[ D = \\frac{P_{AB} - P_{A} P_{B}}{P_{A} P_{B}} = \\frac{5}{12} - \\frac{8}{12}\\times\\frac{6}{12} = \\frac{1}{12} \\] A and B are linked to some extent. LD example 2 \\[ D = \\frac{P_{AB} - P_{A} P_{B}}{P_{A} P_{B}} = \\frac{6}{12} - \\frac{8}{12}\\times\\frac{9}{12} = 0 \\] Here A and B are not linked at all. Basically we are testing whether P(A) and P(B) are independent.","breadcrumbs":"Functional Genomics » Modern Genomics II » Linkage disequilibrium (LD)","id":"30","title":"Linkage disequilibrium (LD)"},"31":{"body":"\\(r^2 = \\frac{D}{P_A P_a P_B P_b}\\) \\(D' = \\frac{D}{D_{\\max}}\\) if \\(D\\) is positive, \\(D' = \\frac{D}{D_{\\min}}\\) if \\(D\\) is negative","breadcrumbs":"Functional Genomics » Modern Genomics II » Relative measures of LD","id":"31","title":"Relative measures of LD"},"32":{"body":"Average proportion of pairwise differences between the sequences Give a multiple sequence alignment, \\(\\pi\\) is defined as \\[ \\pi = \\sum_{i < j} \\frac{\\pi_{ij}}{n_c} \\] where \\(n_c = \\frac{n(n-1)}{2}\\) is the number of pairwise comparisons, and \\(\\pi_{ij}\\) is the proportion of differences between the \\(i\\)th and \\(j\\)th sequences. Below shows an example of \\(\\pi\\) calculation. Nucleotide diversity example \\[ \\pi = \\sum_{i < j} \\frac{\\pi_{ij}}{n_c} = \\frac{\\pi_{12} + \\pi_{13} + \\pi_{23}}{3} = 0.2 \\] Basically just calculating the average number of differences in the matrix.","breadcrumbs":"Functional Genomics » Modern Genomics II » Nucleotide diversity \\(\\pi\\)","id":"32","title":"Nucleotide diversity \\(\\pi\\)"},"33":{"body":"Title: Applications of next-generation sequencing and other genomic techniques Resequencing to identify genetic basis of phenotypic variation Outlier approach Genome-wide association studies ( GWAS ) and linkage disequilibrium Introduction to RNA-seq (transcriptome) focusing on genome duplication Resequencing to detect signature of selection: nucleotide diversity Microbial community and metagenomics, ChIP-seq, epigenomics, whole genome assembly as reference Evolutionary functional genomics can... identify ecologically relevant genes inferring selection & population processes","breadcrumbs":"Functional Genomics » Modern Genomics II » Course contents according to recording","id":"33","title":"Course contents according to recording"},"34":{"body":"Unimportant text is grayed out but worth reading for fluency and context. Motivation RNA species RNA selection methods RNA-seq experiment workflow overview RNA-seq experiment design RNA-seq read mapping methods Considerations How to map reads to a genome? What if we want to map billions of reads? How to deal with SNPs and indels? How to deal with introns (basically very large insertions)? Bowtie TopHat2 STAR Quality control and reporting considerations after mapping PHREAD quality Read trimming Multiple alignments and report considerations Expression quantification How to count reads? EM estimation Alignment-free RNA-seq quantification Normalization","breadcrumbs":"Functional Genomics » Transcriptomics I » Transcriptomics I","id":"34","title":"Transcriptomics I"},"35":{"body":"We are interested in the expression of genes in a cell. Altough proteins are the actors of genes instead of mRNA transcripts, mRNAs transcripts are easier to measure because selection has chosen them to convey the genetic message in a faithful way. Also there are plenty of interesting non-coding RNAs.","breadcrumbs":"Functional Genomics » Transcriptomics I » Motivation","id":"35","title":"Motivation"},"36":{"body":"80% of the total RNA is rRNA. 14% is tRNA. Only 1-3% is mRNA. All other species account for the remaining 1-3%.","breadcrumbs":"Functional Genomics » Transcriptomics I » RNA species","id":"36","title":"RNA species"},"37":{"body":"RNA selection methods A: total RNA Unbiased estimation Dominate by rRNA, not very informative B: ribosomal reduction/depletion Use probes that bind to rRNA and pull them out < 5% rRNA left C: poly-A selection Use probes that bind to poly-A tails Selects for mRNA, and also some long non-coding RNAs (because they also have poly-A tails) D: cDNA capture Design target probes that bind to a certain set of RNAs Limited transcriptome coverage 90% of transcriptome research utilize poly-A selection; 5% of them go for ribosomal depletion because their mRNAs are of low quality and fragmented. The rest 5% do have high-quality mRNAs but still go for ribosomal depletion because they want to estimate other RNA species at the same time. Note: current illumina sequencers cannot sequence miRNAs (20-25nt) and mRNA fragments (100-300nt) together (because of the large length discrepency)","breadcrumbs":"Functional Genomics » Transcriptomics I » RNA selection methods","id":"37","title":"RNA selection methods"},"38":{"body":"A typical RNA-seq experiment workflow is shown below. Typical RNA-seq experiment We can do either single-read sequencing or paired-end sequencing (as is shown in the figure above) in the third step. It can also be summarized into a flow diagram. The following sections will go into more details about each step.","breadcrumbs":"Functional Genomics » Transcriptomics I » RNA-seq experiment workflow overview","id":"38","title":"RNA-seq experiment workflow overview"},"39":{"body":"RNA-seq experiments are implemented as comparative experiments RNA-seq is used to measure the relative abundance (expression) of each mRNA (gene) in a sample sample: We cannot sequence all the RNA fragments. Instead, we randomly select about 20M fragments as a representation of the total RNA obtained. Note that we can sample multiple times. RNA-seq can link gene expression to genotype phenotype treatment response","breadcrumbs":"Functional Genomics » Transcriptomics I » RNA-seq experiment design","id":"39","title":"RNA-seq experiment design"},"4":{"body":"Biofluiddynamics Synthetic Biology I","breadcrumbs":"Home » 24FS","id":"4","title":"24FS"},"40":{"body":"","breadcrumbs":"Functional Genomics » Transcriptomics I » RNA-seq read mapping methods","id":"40","title":"RNA-seq read mapping methods"},"41":{"body":"Ideally, the read mapping process is as simple as sequencing the transcribed RNAs and then mapping the sequences back to the genome to identify the gene expression. However, in reality, the process is much more complicated because current sequencers can only perform faithful sequencing up to a couple of hundreds of bp (usually 200-800bp), and a typical mRNA is 2-3kb long. Thus, the mRNA needs to be first chopped into fragments and then sequenced. When we do the mapping, we're mapping the chopped reads back to the genome instead of the whole spliced sequences. The existence of alternative splicing (protein isoforms) and sequencing errors makes the mapping process even more complicated. While discussing the mapping process, those limitations and problems should be kept in mind. How to map reads to a genome? Mapping algorithms must be Fast Thus usually find perfect or near-perfect (tolerating 1bp mismatch) match Able to handle SNPs, indels and sequencing errors We can always perform sequence alignment (here needs local alignment/ Smith-Waterman alignment ). Of course the score matrix should be good to determine the correct alignment. But this is slow because it requires quadratic efforts. What if we want to map billions of reads? Indexing method Reads are aligned by index lookup instead of $O(n^2)$ seq comparison Usually hashed so the lookup time is much faster If lookup fails, actual sequence comparison is performed (more details on this in next chapter) Major aligners use the Burrows-Wheeler transform (BWT) to index the reference genome Very small. Even for the human genome the index fits into 3GB RAM. Example aligners bowtie , bowtie2 BWA TopHat2 STAR SOAP ... How to deal with SNPs and indels? SNPs Can always be handled by performing real Smith-Waterman alignment but expensive At mismatched positions, try all possible bases and search the BWT index again Computing effort grows exponentially Gapped alignment Chop reads into short segments (seeds) align those seeds in a mismatch-free manner (typically using BWT index lookup again) stitch them back together Might require multiple rounds of chopping Indels Can only be found with gapped alignment (described above), BWT lookup is not enough How to deal with introns (basically very large insertions)? Approaches Map directly to trapscript sequences (no intron) not to the genome Pro: introns are not a problem Cons: unknown genes/isoforms cannot be detected Spliced alignment to genome Pro: finds reads from unknown gene loci or unknown isoforms Con: larger search space, potentially more false positives, wrong alignment to pseudogenes Combination of above Difference between spliced alignment and gapped alignment Gapped alignment: longer gaps means high score penalty and lower score Spliced alignment: long gaps at canonical splice-sites are allowed, but lacking canonical splice-sites or gaps elsewhere (at non-canonical splice sites) are penalized Pseudogenes associated retrotransposed spliced sequence of a certain gene, thus intron-free , and appears \" exonic \" Have almost the same sequence as the original gene Not functional because they do not have access to promotors so won't be transcribed Usually contain more mutations because there are no selection pressures to keep them intact Exonic reads will map to both the gene and its pseudogene, but likely preferring gene placement due to lack of mutations A spliced read could be incorrectly assigned to the pseudogene as it appears to be exonic, preventing higher scoring spliced alignments from being pursued","breadcrumbs":"Functional Genomics » Transcriptomics I » Considerations","id":"41","title":"Considerations"},"42":{"body":"Bowtie Step-by-step backward searching the suffix of the query sequence in the BWT index Exact matching Searched suffix appears consecutively in BWT The size of range in BWT shrinks or remains the same almost does not handle mismatches ; a single mismatch will lead to empty BWT range / failed index lookup mismatches can come from Sequencing error (illumina: $1/1000$) True variation (SNPs, human mutation rate $\\approx 1/10^4$ mismatches are not rare events! at least 10% of >100nt reads Empty BWT range activates backtracking All possible bases are tried at the mismatched position Gapped alignment","breadcrumbs":"Functional Genomics » Transcriptomics I » Bowtie","id":"42","title":"Bowtie"},"43":{"body":"Handles mismatches by gapped alignment. It first performs (optional) transcriptome alignment (exonic), and then performs genome alignment for the unmapped reads. The unmapped reads in the second step are multi-exon spanning reads and undergo spliced alignment by chopping the reads into even shorter segments and splice site identification etc. The figure is too complicated, not recommended to go into details but still attached here for reference. TopHat2 pipeline","breadcrumbs":"Functional Genomics » Transcriptomics I » TopHat2","id":"43","title":"TopHat2"},"44":{"body":"Direct alignment of non-contiguous sequences to the reference genome. First find Maximal Mappable Prefix (MMP) of the read MMP is the longest prefix of the read that can be mapped to the reference genome MMP is found by searching the BWT index Possible to tolerate a certain degree of mismatches using extend mode Stop extending MMP if MMP covers the whole read or encounters a mismatch In the second case, find the MMP of the remaining suffix of the read Repeat until the whole read is covered Possible to use trim mode to get rid of A-tail or adapter sequence","breadcrumbs":"Functional Genomics » Transcriptomics I » STAR","id":"44","title":"STAR"},"45":{"body":"","breadcrumbs":"Functional Genomics » Transcriptomics I » Quality control and reporting considerations after mapping","id":"45","title":"Quality control and reporting considerations after mapping"},"46":{"body":"Each called base is given a quality score $Q$ $Q = -10 \\log_{10}(p)$ (PHRED score) $p$ is the estimated probability of the base being called incorrectly $Q$ is the negative log of the probability Q-score = 10: prob = 0.1 Q-score = 20: prob = 0.01 Q-score = 30: prob = 0.001 Q30 is often used as a cutoff for high quality reads How to use: downweight the low-quality bases when computing the alignment score First introduced for capillary sequencers PHRED scores are determined by the sequencer that directly rates how reliable the measured signal is","breadcrumbs":"Functional Genomics » Transcriptomics I » PHREAD quality","id":"46","title":"PHREAD quality"},"47":{"body":"Not all parts of the read are useful for alignment. It is common to trim the reads. Reasons for trimming: Systemetic errors of sequencer Illumina sequencers have high error rate at the first few bases Basically all sequencers have increasing error rate towards the end of the read Adapter trimming If the inserted DNA/RNA fragment is too short, the read will contain part of the adapter (since the sequencer generally will sequence 100bp at each end) Can be challenging if: The inserted sequence is 90-100bp -- the incorporated adapter sequence will only be a few bp long The read has many sequencing errors 3'-bias / degradation The 3' end of the read is generally more likely to be degraded than the 5' end Depending on RNA degradation and extration protocols reads may not be equally distributed along the transcripts Trimming methods Hard trimming : trim a fixed number of bases from the beginning and/or end Quality trimming : cut the end of the read as soon as the base quality drops below a threshold Soft trimming : trim the read that cannot be aligned to the reference genome","breadcrumbs":"Functional Genomics » Transcriptomics I » Read trimming","id":"47","title":"Read trimming"},"48":{"body":"A read may have multiple valid alignments with identical or similarly good alignment scores Aligners may use different reporting strategies: Randomly select one alignment from the top-scoring alignments Report all alignments that are within delta of the top-scoring alignment; clip if more than $N_{max}$ alignments are found Report only alignments if they are unique (no other alignment within delta of the alignment score) Do not report anything if more than $N_{max}$ valid alignments are found … Whether a read has a unique alignment depends on the read sequence and the sequence homology of the organism the search algorithm of the aligner Whether a read has a single reported alignment depends additionally on the reporting options strategy of the aligner","breadcrumbs":"Functional Genomics » Transcriptomics I » Multiple alignments and report considerations","id":"48","title":"Multiple alignments and report considerations"},"49":{"body":"Expression quantification on Gene level Reads belong to a gene locus Isoform level Reads belong to an isoform","breadcrumbs":"Functional Genomics » Transcriptomics I » Expression quantification","id":"49","title":"Expression quantification"},"5":{"body":"","breadcrumbs":"Mobile Health and Activity Monitoring » Mobile Health and Activity Monitoring","id":"5","title":"Mobile Health and Activity Monitoring"},"50":{"body":"Unique mapped reads Multi-reads are ignored – potentially biased quantification All mapped reads Assignment of multi-reads need abundance estimation of overlapped genes/isoforms Read counting EM estimation General steps Estimate abundances based on uniquely mapping reads only For each multi-read, divide it between the transcripts to which it maps, proportionally to their abundances estimated in the first step Recompute abundances based on updated counts for each transcript r. Continue with Step 2 Model the sequencing and analysis process with a likelihood function E-step: Compute expected read counts given current expression levels M-step: Compute expression values maximizing likelihood given expected read counts Alignment-free RNA-seq quantification Instead of building BWT, we build hashed k-mer index based on known transcriptome, and search the k-mers in the reads to map and compute abundance. Easier to understand through side-by-side comparison with the traditional alignment dependent method: Alignment dependent v.s. alignment free While allocating k-mer to transcript, we try to make each transcript covered as uniformly as possible. Pros Accurate and fast in quantifying KNOWN TRANSCRIPTS Counts can be aggregated to get gene-level quantification Cons Less well annotated genomes – less accurate results No alignments – no information about SNPs Transcript coverage is not uniform","breadcrumbs":"Functional Genomics » Transcriptomics I » How to count reads?","id":"50","title":"How to count reads?"},"51":{"body":"","breadcrumbs":"Functional Genomics » Transcriptomics I » Normalization","id":"51","title":"Normalization"},"52":{"body":"Methods of Exploratory Data Analysis Clustering Distance measures Hierarchical Clustering k-means Clustering Comparison of Hierarchical Clustering and k-means Clustering Dimensionality Reduction Principal Component Analysis (PCA) t-SNE UMAP Differential Expression Analysis","breadcrumbs":"Functional Genomics » Transcriptomics II » Transcriptomics II","id":"52","title":"Transcriptomics II"},"53":{"body":"Typical shape of data we have in hand: a data matrix. Data matrix where the columns are the samples and the rows are the features (usually gene expressions). (It can be the other way around, but this is the most common case.) Clustering Hierarchical clustering k-means clustering Dimensionality reduction Matrix Factorization PCA MDS (Multidimensional Scaling) Graph-based methods t-SNE UMAP","breadcrumbs":"Functional Genomics » Transcriptomics II » Methods of Exploratory Data Analysis","id":"53","title":"Methods of Exploratory Data Analysis"},"54":{"body":"Goals group similar samples evaluate similarity between expression profiles of the samples test if similarities match the experimental design and effect sizes test if variations within condition is smaller than between conditions outliers detection group similar genes guilt by association : infer functions of unknown genes from known genes with the same expression pattern (co-expression)","breadcrumbs":"Functional Genomics » Transcriptomics II » Clustering","id":"54","title":"Clustering"},"55":{"body":"To cluster samples, we need to first define a \"distance\" measure between samples. Commonly used distance measures: Euclidean distance (typically for clustering samples) Euclidean distance of two profiles $\\mathbf{x}$ and $\\mathbf{y}$ with $p$ genes (i.e. the distance between two $p$-dimensional vectors $\\mathbf{x}$ and $\\mathbf{y}$) $d(\\mathbf{x}, \\mathbf{y}) = \\sqrt{\\sum_{i=1}^{p} \\left(x_i - y_i\\right)^2}$ Expression values MUST BE LOG SCALE $1 - \\text{corr}(\\mathbf{x}, \\mathbf{y})$ (typically for clustering genes) Correlation coefficient of two profiles $\\mathbf{x}$ and $\\mathbf{y}$ with $p$ samples $\\text{corr}(\\mathbf{x}, \\mathbf{y}) = \\frac{\\sum_{i=1}^{p}(x_i - \\bar{x})(y_i - \\bar{y})}{\\sqrt{\\sum_{i=1}^{p}(x_i - \\bar{x})^2 \\cdot \\sum_{i-1}^{p}(y_i - \\bar{y})^2}}$ $\\bar{x} = \\frac{1}{p}\\sum_{i=1}^{p}x_i$ $\\bar{y} = \\frac{1}{p}\\sum_{i=1}^{p}y_i$","breadcrumbs":"Functional Genomics » Transcriptomics II » Distance measures","id":"55","title":"Distance measures"},"56":{"body":"Algorithm : Compute the distance matrix ($n \\times (n - 1) / 2 \\rightarrow O(n^2)$) between all samples Find pair with minimal distance and merge them Update the distance matrix Repeat 2-3 until all samples are merged Parameters : distance measure for samples usually $1 - \\text{corr}(\\mathbf{x}, \\mathbf{y})$ for gene expression distance measure for clusters ( linkage rule ) Single linkage: minimum distance between any elements of the two clusters Complete linkage: maximum distance between any elements of the two clusters Average linkage: average distance between all elements of the two clusters Ward's linkage: minimal increase in intra-cluster variance Input : distance matrix The linkage can be derived directly from the distance matrix. Hence clustering algorithm only needs the distrance matrix as input, not the measurements individually.","breadcrumbs":"Functional Genomics » Transcriptomics II » Hierarchical Clustering","id":"56","title":"Hierarchical Clustering"},"57":{"body":"Algorithm : Randomly assign each sample to one of the $k$ clusters Compute the centroid (cluster center, average of the assigned samples) of each cluster Assign each sample to the cluster with the closest centroid Repeat 2-3 until convergence or a maximum number of iterations Parameters : number of clusters $k$ distance measure for samples Input : data matrix (cannot directly use distance matrix) This method minimizes the intra-cluster variance . Choice of $k$ affects the result.","breadcrumbs":"Functional Genomics » Transcriptomics II » k-means Clustering","id":"57","title":"k-means Clustering"},"58":{"body":"Hierarchical Clustering k-means Clustering Computing time $O(n^2 \\log (n))$ $O(n \\cdot k \\cdot t)$ $t$: number of iterations$k$: number of clusters Memory $O(n^2)$ $O(n \\cdot k)$ When clustering large numbers of genes (>1e4, hierarchical clustering is not practical","breadcrumbs":"Functional Genomics » Transcriptomics II » Comparison of Hierarchical Clustering and k-means Clustering","id":"58","title":"Comparison of Hierarchical Clustering and k-means Clustering"},"59":{"body":"","breadcrumbs":"Functional Genomics » Transcriptomics II » Dimensionality Reduction","id":"59","title":"Dimensionality Reduction"},"6":{"body":"A course collectively taught by multiple professors. Multiple-choice exam, lots of memorization.","breadcrumbs":"Functional Genomics » Functional Genomics","id":"6","title":"Functional Genomics"},"60":{"body":"Goal : Find a new coordinate system such that the first axis (principal component) captures the most variance, the second axis captures the second most variance, and so on. The data is linearly transformed to a new coordinate system.","breadcrumbs":"Functional Genomics » Transcriptomics II » Principal Component Analysis (PCA)","id":"60","title":"Principal Component Analysis (PCA)"},"61":{"body":"Algorithm : In the high-dimensional space, create a probability distribution that dictates how likely two points are to be neighbors. Recreate a low dimensional space that follows the same probability distribution as best as possible. How to find the best low-dimensional representation: preserve the pairwise distances between neighboring points in the high-dimensional space non-linear, different transformations on different regions Characteristic: Powerful, but need to fiddle with random seed and perplexity Non-deterministic","breadcrumbs":"Functional Genomics » Transcriptomics II » t-SNE","id":"61","title":"t-SNE"},"62":{"body":"Uniform Manifold Approximation and Projection Approach: Find for each point the neighbors and build simplices (simplex: a generalization of the concept of a triangle or tetrahedron to arbitrary dimensions) and then optimize the low-dimensional representation to preserve the simplices.","breadcrumbs":"Functional Genomics » Transcriptomics II » UMAP","id":"62","title":"UMAP"},"63":{"body":"","breadcrumbs":"Functional Genomics » Transcriptomics II » Differential Expression Analysis","id":"63","title":"Differential Expression Analysis"},"7":{"body":"01. Modern Genomics I 02. Modern Genomics II 03. Transcriptomics I 04. Transcriptomics II 05. miRNAs and Other Small RNAs 06. Proteomics 07. Metabolomics 08. Single Cell Mass Cytometry 09. Protein Networks 10. Epigenomics and Gene Regulation 11. Quality Control and Standards","breadcrumbs":"Functional Genomics » Table of Contents","id":"7","title":"Table of Contents"},"8":{"body":"Introduction Timeline Why Genomics? Comparative genomics use case examples Classical sequencing method Sanger (double-deoxy) sequencing Automated Dye Sequencing New (Next-generation) sequencing technologies Amplification technologies Emulsion PCR PCR on solid support Barcoding and \"linked reads\" Sequencing technologies Pyrosequencing Reversible terminator sequencing Sequencing by semi-conductor Current implementations of NGS Third-generation sequencing technologies Environmental sequencing How to deal with environmental sequencing data Single-cell sequencing Why? How? Single-cell isolation Whole genome amplification Genomic databases","breadcrumbs":"Functional Genomics » Modern Genomics I » Modern Genomics I","id":"8","title":"Modern Genomics I"},"9":{"body":"Molecular biology is governed by the \"central dogma\". Genomics is basically studying the DNA part of it. 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