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ChangeLog
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170328 Martin Mann :
* PredictorHeuristic* :
* predict() :
* bugfix : reinit was not overwriting all matrix entries
(thanks to Alex Gawronski)
170307 Martin Mann :
* header defines prefixed with INTARNA_
* general.h :
+ checks if defines with general names are already present
* intarna specific defines prefixed with INTARNA_
* configure.ac :
* VRNA configure flag conform with LocARNA (--with-vrna)
* README.md
+ (minimal) library information added
* CommandLineParsing :
+ argument boundaries for outDeltaE and outMaxE
* SeedHandler :
* traceBackSeed() :
* bugfix: was not using offset1/2
170306 Martin Mann :
+ src/IntaRNA : subfolder that holds all libIntaRNA related sources
+ "IntaRNA" namespace for all libIntaRNA sources
+ libIntaRNA.a build
* tests adapted to library usage
* configure.ac :
+ pkg-config based VRNA version check (optional)
+ --disable-pkg-config switch
* tests rewritten using AS_IF()
+ AC_CONFIG_MACRO_DIR() replaces individual m4_include() calls
+ VRNA_REQUIRED_VERSION variable
+ AC_PROG_RANLIB
+ pkg-config related files and commands
170227 Martin Mann :
* InteractionEnergy :
+ getE_multi() : generic function to get the energy contribution of a
intramolecularly structured gap between two interaction sites
* InteractionEnergy :
* InteractionEnergyBasePair :
* InteractionEnergyIdxOffset :
* InteractionEnergyVrna :
- getEU() : renamed to getE_multiUnpaired()
+ getE_multiUnpaired() : former getEU()
+ getE_multiHelix() : penalty for the intermolecular site that is part of the
intermolecular multiloop as a helix (right interaction site)
+ getE_multiClosing() : penalty for closing the multi-site gap (on the left)
##### version 2.0.1
170221 Martin Mann :
* PredictionTrackerPairMinE :
* writeData() :
* column order reversed to be index ascending
170219 Martin Mann :
* RnaSequence :
+ operator == : equality check (id,length,seq)
* PredictionTrackerPairMinE :
* writeData() :
+ col/row header now includes sequence position beside according nucleotide
* PredictionTrackerProfileMinE :
* writeProfile() :
+ additional column for according nucleotide
* CommandLineParsing :
+ getFullFilename() : provides the fill in/output file name given a suffix,
i.e. adding a sequence specific prefix if needed
* validate_?AccFile() :
+ getFullFilename() usage for multi-sequence accessibility input
+ additional check to hinder STDIN-based multi-sequence accessibility input
* write*Accessibility() :
+ getFullFilename() usage for multi-sequence accessibility output
* construction() :
- ?AccFile : no validation on parsing (requires prior full sequence parse)
* parse() :
+ ?AccFile validation after sequence parsing is done
* bugfix: *AccConstr presence check corrected
* *Acc : accessibility load from file for multi-sequence input enabled
- generation of additional output files for multi-sequence input enabled
* get*Accessibility() :
+ getFullFilename() usage for multi-sequence accessibility input
* getPredictor() :
+ getFullFilename() usage for multi-sequence prediction tracking output
170217 Martin Mann :
* README.md :
+ outfile section
+ minE profile docu
* accessibility output corrected
+ doc/figures/profile-minE.png : minE profile example
* CommandLineParsing :
- out*File : replaced by --out multi-arg handling
- validate_out*File() : obsolete
+ OutPrefixCode : encodings for all valid prefixes of --out
+ getCodeForPrefix() : provides the OutPrefixCode for a given prefix string
+ outPrefix2streamName : holds for each registered --out prefix the user
provided file/stream name or an empty string if not provided
(filled by validate_out())
* out : now a vector of arguments to enable multi-arg occurrences
* write*Accessibility : uses now outPrefix2streamName values
* constructor :
+ initialization of outPrefix2streamName
* argument help unified
* parse() :
+ duplication check for --out arguments to avoid file write clashes
+ PredictionTrackerPairMinE enabled
* Interaction :
+ Seed : class to concentrate all seed-related information
- seedRange : replaced by seed member
+ seed : optional Seed object
* setSeedRange() : fills seed member
+ operator=(Interaction) : copy function that creates new seed object
+ copy constructor: to copy seed object
* OutputHandler* :
* adaption to Interaction::Seed change
170214 Martin Mann :
+ PredictionTrackerPairMinE : tracks for all intermolecular index pairs the
minimal energy of any interaction covering this pair
+ PredictionTrackerHub : forwards tracking information to all registered
trackers
* CommandLineParsing :
* getPredictor() :
+ PredictionTrackerHub used for tracker setup
170212 Martin Mann :
* general :
+ newOutputStream() : returns a pointer to a (newly allocated) output
stream depending on the provided string
+ deleteOutputStream() : deletes (if necessary) the pointer returned by
newOutputStream
* CommandLineParsing :
* bugfix : -n argument description wrong [thanks to Michael Uhl]
+ out*minEFile + validator : stream name of minE profile output
* destruction :
+ using deleteOutputStream()
* parse() :
+ using newOutputStream()
+ checks for out*minEfile
* getPredictor() :
+ PredictionTracker setup
* writeAccessibility() :
+ using newOutputStream()
+ using deleteOutputStream()
* InteractionEnergy :
+ getE( Z ) : ensemble energy from partition function
+ OutputHandlerHub : hub for a list of OutputHandler objects to that the output
requests are forwarded
+ PredictionTracker : general interface to track all step results produced by
a Predictor instance
+ updateOptimumCalled() : triggered when a Predictor calls updateOptimum()
+ PredictionTrackerProfileMinE : produces a profile of the minimum interaction
energy for each position of the interacting RNAs (covered by any interaction)
+ stream-based construction
+ filename/streamname-based construction
* Predictor :
+ predTracker : optional PredictionTracker pointer
* constructor :
+ predTracker
* destruction :
+ delete predTracker
* PredictorMfe :
* updateOptimum() :
+ calling predTracker->updateOptimumCalled() if non-NULL predTracker
* PredictorMfe* :
* constructor :
+ predTracker
* PredictorMaxProb* :
* constructor :
+ predTracker
* updateOptimum() :
+ calling predTracker->updateOptimumCalled() if non-NULL predTracker
* using energy.getE( Z )
+ tests : PredictionTrackerProfileMinE
* tests : rename OutputRangeOnly -> OutputHandlerRangeOnly
##### version 2.0.0
170206 Martin Mann :
* src/Makefile.am :
+ AUTOMAKE_OPTIONS = std-options : checks for std options of binary
* tests/Makefile.am :
* tests now build via 'check' make target (autotools-based setup)
* Makefile.am :
* adaptions to test Makefile changes
170203 Martin Mann :
* configure.ac :
+ check for VRNA >= 2.3.0 via function 'vrna_md_copy' exists
* AccessibilityConstraint
+ maxBpSpan + getter : maximal base pair span to be considered for
accessibility computation
* Accessibility* :
- getES() : now part of InteractionEnergy interface
* AccessibilityVrna :
- EsMatrix : moved to InteractionEnergyVrna
- esValues : moved to InteractionEnergyVrna
- computeES() : moved to InteractionEnergyVrna
* constructor() :
- plFoldL : now via AccessibilityConstraint.getMaxBpSpan()
- computeES
* ED >= 0 ensured
* InteractionEnergy :
* getES*() now abstract and to be implemented in subclass
- getES*() implementation based on Accessibility interface
* InteractionEnergyBasePair :
+ getES*() : throws exception since not implemented yet
* constructor() :
+ initES : whether or not to compute precompute ES values
* InteractionEnergyVrna :
* constructor() :
+ initES : whether or not to compute precompute ES values
+ EsMatrix data type
+ esValues1/2 : optional ES value data
+ getES*() : returns esValues* entry if available; throws exception otherwise
+ computeES() : inits ES values based on VRNA routines
* VrnaHandler :
* getModel() :
* uses now vrna_md_copy() (VRNA >= 2.3.0) for model copying
* CommandLineParsing :
* energy :
- 'F' : replaced by 'V'
+ 'V' : VRNA based computation
- OutputMode : replaced by char encoding
* outMode : now char encoding
* OutputHandlerText :
+ detailedOutput : flag to switch between detailed and reduced output
* add() :
+ heads detailedOutput flag
* construction() :
+ detailedOutput flag handling
* PredictorMfe2d :
* initHybridE() :
+ outConstraint argument
* bugfix : maxE check was not considering outConstraint.maxE
* fillHybridE() :
+ outConstraint argument
* PredictorMfe4d* :
* predict :
* bugfix : maxE check was not considering outConstraint.maxE
170202 Martin Mann :
* CommandLineParsing :
* outMaxE maximum now 999 (was 0)
- PredictionMode : replaced by char-based setup
* seedMaxUPq -> seedQMaxUP
* seedMaxUPt -> seedTMaxUP
* seedRangeq -> seedQRange
* seedRanget -> seedTRange
+ pred + validator : setup of prediction target (mfe-si, maxprob-si, ...)
* predMode :
* char-based setup
- max-prob mode (now selected via --pred=P)
* outOverlap : char-based setup
* outAccFileq -> outQAccFile
* outAccFilet -> outTAccFile
* outPuFileq -> outQPuFile
* outPuFilet -> outTPuFile
* get*Accessibility() :
* computeES setup now via pred.val
* getPredictor() :
+ support for different prediction targets via pred.val switch
* OutputConstraint :
* constructor() :
- (maxE < 0) check removed
+ intarna_config.h.in : header containing package version and configure
information
* configure.ac :
+ generate intarna_config.h
+ AC_SUBST(INTARNA_MULITHREADING)
* AccessibilityDisabled :
* getES() :
- no error is thrown anymore
* perl/*.pl : adaptions to CLI changes
170201 Martin Mann :
* CommandLineParsing :
* max sequence number now 99999
* setup of threads parameter only if INTARNA_MULITHREADING
* configure.ac :
+ --disabled-multithreading : sets INTARNA_MULITHREADING to 0, otherwise 1
* enclose all OMP stuff with INTARNA_MULITHREADING preprocessor checks
* AccessibilityVrna :
* computeES() : bugfix
170131 Martin Mann :
* CommandLineParsing :
+ opts_cmdline_short : short option list for abbreviated help output
* constructor() :
+ setup of opts_cmdline_short
* parse()
+ handling of short and full help output
+ disallow multi-threading for IntaRNA v1 output (due to separators)
* q|tAcc : renamed 'F' option to 'C' for 'computation of accessibilities'
* adaption to OutputHandlerIntaRNA1* rename
+ OutputMode::V1_NORMAL : normal version 1.* output
+ threads + validate + getter : OMP max thread number
- OutputHandlerIntaRNA1detailed : renamed to OutputHandlerIntaRNA1
+ OutputHandlerIntaRNA1 : former OutputHandlerIntaRNA1detailed
+ detailedOutput : flag to switch between detailed and normal v1 output
+ OMP : ensure no parallel write to output stream
* perl/IntaRNA*_1ui.pl :
+ normal output enabled (-o flag now with effect)
* intaRNA :
* adaption to OutputHandlerIntaRNA1* rename
+ OMP : parallelization of target/query processing
+ OMP : exception handling within parallelized loops due to missing OMP
exception forwarding
* final exception handling now always returns -1 (even in debug mode)
* OutputHandlerCsv :
+ E_loops output
+ OMP : ensure no parallel write to output stream
* OutputHandlerText :
+ OMP : ensure no parallel write to output stream
* AccessibilityVrna :
+ OMP : ensure no parallel VRNA-calls since not threadsafe
+ m4/m4_ax_openmp.mp4 : OMP checks
* configure.ac :
- backward compatibility stuff for autoconf < 2.65
+ OMP check and AM_CXXFLAGS setup
170130 Martin Mann :
* CommandLineParsing :
+ stdinUsed : flag to ensure STDIN is used for input only once
+ setStdinUsed() : sets stdinUsed = true if not already or throws log
otherwise
* q/tAcc :
+ 'P' : unpaired probabilities in RNAplfold style from --q/tAccFile
+ 'E' : ED values in RNAplfold-Pu-like style from --q/tAccFile
+ validate_q/tAccFile()
* get*Accessibility() :
+ AccessibilityFromStream support
* bugfix : maxLength setup has to be = min(maxLength,accW)
+ outAccFile* + validate : output ED values to file/stream
+ outPuFile* + validate : output Pu values to file/stream
+ validate_outputTarget() : generic text function for stream names
* validate_out() : calls validate_outputTarget()
+ write*Accessibility() : write the given accessibility to file/stream if
requested by the user
+ writeAccessibility() : writes accessibility data to file/stream in the
requested format
* q/tIntLenMax argument info :
+ information that --q/tAccW might overwrite
* Accessibility :
* getMaxLength() : return value non-const size_t
+ writeRNAplfold_ED_text() : Pu output in RNAplfold style
+ writeRNAplfold_Pu_text() : ED output in RNAplfold style
+ writeRNAplfold_text() : generic RNAplfold Pu-styled text output
* AccessibilityFromStream :
+ InStreamType::ED_RNAplfold_Text : ED input in RNAplfold style
+ parseED_RNAplfold_text() : read ED input in RNAplfold style
* parsePu_RNAplfold_text() : using parseRNAplfold_text()
+ parseRNAplfold_text() : generic RNAplfold Pu-styled text input
+ reduces availMaxLength if not enough data in input and outputs a user
information
+ availMaxLength : stores the maximal window length parsed from the input,
init = Accessibility::getMaxLength()
+ getMaxLength() : provides availMaxLength
* AccessibilityVrna :
* getED() :
+ accessibility constraint check
* AccessibilityConstraint :
+ isAccessible( range )
+ isMarkedAccessible( range )
+ isMarkedBlocked( range )
+ isUnconstrained( range )
* README.md :
+ docu for read/write of ED and Pu values for accessibility initialization
170129 Martin Mann :
* PredictorMfe2dHeuristic* :
* fillHybrid*() :
+ interaction length check before energy evaluation
170128 Martin Mann :
* Makefile :
+ info for testing directive
* AccessibilityDisabled :
* constructor :
- defaults removed
* AccessibilityVrna :
* constructor :
* argument order changed
+ AccessibilityFromStream : populates ED values from stream
+ InStreamType::Pu_RNAplfold_Text
+ parsePu_RNAplfold_Text() : parse RNAplfold unpaired probability text output
* CommandLineParsing :
+ q/tAccFile : file/stream to read accessibilities from
+ q/tAcc :
+ 'P' : read unpaired probability from file : RNAplfold text output
+ stream name checks now case insensitive
170127 Martin Mann :
* SeedConstraint :
+ maxED + getter : maximal ED value per sequence for a seed region
* constructor ()
+ maxED
* SeedHandler :
* fillSeed() :
+ skip seed regions with ED > maxED
* RnaSequence :
* SequenceAlphabet order changed
* OutputHandlerText :
* add() :
+ seed ED values added
* OutputHandlerCsv :
+ Pu, seedPu, start/end, ED, E_*, seedStart/End, seedED
* id : replacement of colSep occurrences
* CommandLineParsing :
+ seedMinPu + validator
* constructor() :
+ seedMaxED argument
* outCsvCol : + spaces to unlink ID list
* outCsvCols_default = id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E
* intaRNA :
+ storing of queryAcc object to avoid recomputation for different targets
170126 Martin Mann :
* Interaction :
+ dotBracket() : converts to VRNA-like dot-bracket notation
+ dotBar() : converts to position+interaction encoding using dot and bar
+ dotSomething() : generic function to generate substrings for dotBracket()
and dotBar()
* test/Interaction :
+ dotBracket()
+ dotBar()
* PredictorMfe :
* reportOptima() :
* bugfix : nextBest() called too often
* OutputHandlerText :
* add(range) inlined
+ OutputHandlerCsv : produces customizable CVS table output
* CommandLineParsing :
* OutputMode :
+ CSV
+ outCsvCols* + validator : argument variable + default value
+ initOutputHandler() : prints initial output
* constructor :
* outMode argument : support for CSV
+ outCsvCols argument
* out argument : short option removed
* parse() :
+ parseStyle setup to guide parsing
- intial output moved to initOutputHandler()
+ initOutputHandler() call
+ CSV check
* getOutputHandler() :
+ CSV
* intaRNA :
+ generic exception handling
170125 Martin Mann :
* perl/*.pl :
* bugfix : -L setup was using -w argument
170123 Martin Mann :
* AccessibilityVrna :
* fillByConstraints() : bugfix of line shift for ED filling
* fillByRNAplfold() :
* fillByRNAup() :
+ explicit handling of Pu == 0 to trigger ED = ED_UPPER_BOUND
* intaRNA :
* debug exception catch message extended (debugger hint)
* PredictorMfe2dHeuristic :
* PredictorMfe2dHeuristicSeed :
* traceBack() : bugfix : right boundary (j1,j2) could be inserted again
* loop check simplified
* CommandLineParsing :
* fix of plfold L <= W check (only enabled if W>0)
170122 Martin Mann :
* AccessibilityVrna :
* fillByRNAplfold : bugfix memleak (pl return value not freed)
* consistent use of CLEANUP() to deallocate memory allocations done via 'new'
* intaRNA :
* global try-catch-block now always enabled but forwards exception in debug
mode (for debugger use)
* PredictorMaxProb* :
* PredictorMfe4d* :
* clear() : bugfix memleak (4th dimension not freed)
* RnaSequence :
* SequenceAlphabet now 'ACGUN' to simplify checks
170120 Martin Mann :
* Accessibility :
+ getES() : computes the ensemble energy of all local structures of a
subsequence under the assumption that the subsequence is part of a
multiloop
* AccessibilityDisabled :
+ getES() : throws an exception since not computable
* AccessibilityVrna :
+ EsMatrix type = triangular matrix
+ esValues : stores ES values if non-NULL
+ getES() : computed via McCaskill algorithm
* constructor() :
* vrnaHandler now const
+ computeES argument to trigger ES computation
* RNAup-based ED computation also when plFoldW > seqLength
+ computeES() : computes the ES values via VRNA 3 interface
* CommandLineParsing :
* get*Accessibility() :
+ computeES flag = true in DEBUG mode (has to be replace by predictor
selection based setup)
* InteractionEnergy :
* getES*() : now implemented based on accS*.getES()
+ getEU() abstract : energy for k unpaired bases within a multiloop
* InteractionEnergyBasePair :
- getES*() : implemented in superclass
+ getEU() : returns 0
* InteractionEnergyIdxOffset :
+ getEU() forward
* InteractionEnergyVrna :
- getES*() : implemented in superclass
+ getEU() : returns k * VRNA.MLbase
* ReverseAccessibility :
+ getES() forward
170119 Martin Mann :
* CommandLineParsing :
+ out : output stream selection
+ outStream : output stream to write to
+ argument 'outMode' : former 'out'
* argument 'out' now sets output stream
* getOutputStream() : returns now outStream
* destructor()
+ deletion of outStream if file stream
* parse() :
+ creation of file stream for output if out != STDOUT|STDERR
* perl/*.pl :
* adaptions to argument change
170118 Martin Mann :
* CommandLineParsing :
* validate_sequenceArgument() :
* parseSequences() :
* uses now RnaSequence::isValidSequenceIUPAC()
170117 Martin Mann :
* RnaSequence :
* SequenceAlphabet : now 'ACGU' only
+ SequenceAlphabetIUPAC : all IUPAC-conform nucleotide encodings
* areComplementary() :
* getCodeForChar() :
* getUpperCase() :
+ checks in debug mode only
* isAmbiguous() :
* check reduced to 'N'
* RnaSequence() :
* ambiguity check uses now converted sequence
+ isValidSequenceIUPAC() : check for IUPAC conformity
* CommandLineParsing :
* validateSequenceAlphabet() :
* now checks with RnaSequence::isValidSequenceIUPAC()
+ information about IUPAC sequence encoding
170111 Martin Mann :
* CommandLineParsing :
* IntaRNA v1 input details corrected
161230 Martin Mann :
* CommandLineParsing :
* parseSequencesFasta() :
+ bugfix : was not reading final lines without newline at the end
* OutputHandlerIntaRNA1detailed :
* output corrected
161229 Martin Mann :
* CommandLineParsing :
* IntaRNA_v1_detailed init output now more like v1 output
* PredictorMfe2dHeuristic* :
* getNextBest() :
* bugfix : seq1 range overlap check
* PredictorMfe4d :
* getNextBest() :
* bugfix : getE() using wrong index order
* PredictorMfe4dSeed :
* getNextBest() :
* bugfix : getE() using wrong index order
* predict() :
* bugfix : hybridE_seed resize missing
* fillHybridE_seed() :
+ additional early check for too small interaction sites (no seed)
* traceBack() :
* bugfix : energy check right of seed corrected
* bugfix : check entry existence before access
* intaRNA :
+ exception catch + handling only in non-debug mode (eases debug)
161224 Martin Mann :
* OutputHandler :
+ reportedInteractions : count of reported interactions
+ reported() : returns reportedInteractions
* intaRNA :
+ setup of separator output for IntaRNA v1 output
* OutputHandlerIntaRNA1detailed :
+ intialOutputDone : tag to store whether or not something was already done
+ prinSeparator : tag whether or not a separator is to be printed
* constructor()
- initial output (now part of add())
* add()
+ initial output for first reported interactions
+ counting of non-empty interactions
+ addSeparator() : sets printSeparator
161222 Martin Mann :
* perl/IntaRNA_1ui.pl :
- seed energy restriction (only needed to mimic IntaRNA v1 behaviour)
+ output mode setup
* CommandLineParsing :
+ OutputMode : enum for different output modes
+ PredictionMode_min/max
+ outMode + validator : output mode argument variable
* predMode : init via min/max enum entries
* constructor :
* argument values via toString() and enum entries to be consistent
+ '--out,-o' : argument to setup output mode
* parse() :
+ IntaRNA1_detailed input output
* getOutputHandler() :
- IntaRNA1_detailed input output
+ switch based on outMode.val
* getPredictor() :
+ PredictorMfe4dSeed support
* OutputHandlerIntaRNA1detailed :
* output corrected
+ perl/IntaRNA_up_1ui.pl : IntaRNA v1-styled interface wrapper for IntaRNA_up,
i.e. RNAup like computation (4d space&time) including seed constraints
+ PredictorMfe4dSeed : seed-constraint incorporating full RNAup-like predictor
161221 Martin Mann :
* RnaSequence :
* SequenceAlphabet += tT
* getUpperCase() :
* replacement of 'T' with 'G'
* Predictor :
* updateOptima() : additional flag to avoid recomputation of overall energy
* PredictorMfe2dHeuristic* :
* fillHybridE() :
+ temporary vars to reduce full energy recomputation
* SeedHandler :
* fillSeed() :
+ returns now the number of valid seeds found
* PredictorMfe2dHeuristicSeed :
* predict() :
+ stops computation if
+ no seed interaction possible
+ mfe without seed not < outConstraint.maxE
* SeedHandler :
* best hybrid energy now via table access (avoid recomputation)
* Predictor*Seed :
* bugfix : reported seed energy missed E_init term
* OutputHandlerIntaRNA1detailed :
* bugfix : newline missing at end of each interaction output
161219 Martin Mann :
* src/Makefile :
* bin file name changed to "IntaRNA"
* .travis : bin file name changed
+ perl/IntaRNA-1ui.pl : wrapper to enable IntaRNA v1 like parameter usage
* OutputConstraint :
+ maxE : maximal energy to be reported
* CommandLineParsing :
+ outMaxE + validator : argument for maximal energy of reported interactions
* PredictorMfe :
* initOptima() : initializes with OutputConstraint.maxE
* reportOptima() : ensures energy is below OutputConstraint.maxE
* .gitignore :
+ .* : all hidden files ignored
+ perl/Makefile.am
+ perl wrapper packaging and install
* configure.ac :
+ perl/Makefile
161216 Martin Mann :
* README.md
+ feature comparison table started
+ configure.ac :
* -fopenmp now always added to CXXFLAGS (also if VRNA path not specified)
+ OutputHandlerIntaRNA1detailed : output similar to IntaRNA v1.2.*
* CommandLineParsing :
* getOutputHandler() :
+ temporarily : init output of IntaRNA 1.* mode
* temporarily : IntaRNA 1 output
+ getOutputStream() : stream to be passed to OutputHandler instances
161215 Martin Mann :
* AccessibilityConstraint :
* construction : bugfix reverse handling
* CommandLineParsing :
* getSeedConstraint()
+ now with energy argument arguments to access seed lengths
+ reverses seed ranges for seq2
* IndexRangeList :
* List now std::list (before std::vector)
+ covers(range) + tests
+ reverse() + tests : reverses the indices and range order
* PredictorMfe2d :
* PredictorMfe2dSeed :
* predict() : bugfix : throw without "new"
* Predictor*Seed :
* bugfix : uses now SeedHandlerIdxOffset instead of SeedHandler
+ seed handler offset setup
* RnaSequence :
* areComplementary() : bugfix : throw without "new"
* SeedConstraint :
* members not const (otherwise getter not needed)
+ getRanges*() : write access for ranges
* SeedHandler :
* public functions virtual
+ offset* : index offset (needed for restricted matrices)
* fillSeed() :
* bugfix : sanity checks corrected
* bugfix : index offset was missing
* traceBack() :
* bugfix : index offset was missing
+ SeedHandlerIdxOffset : index shift wrapper for SeedHandler
161214 Martin Mann :
* intaRNA :
* query/target enumeration swapped, such that seq1 == target in prediction
and output
* OutputConstraint : data structure defining all output constraints
+ enum ReportOverlap : 4 possibilities where overlapping is allowed
+ reportMax : max number of (suboptimal) interactions to report
+ reportOverlap : the overlap constraint for reported interactions
+ deltaE : maximal energy difference to mfe to be reported
* Predictor :
* reportMax/reportNonOverlapping replaced by outConstraint
* predict()
* initOptima()
* reportOptima()
* IndexRange :
+ regex : regex to match valid string encoding
+ fromString() : parse string encoding
+ operator == ()
+ operator != ()
* operator << () : now regex conform
* IndexRangeList :
+ regex : regex to match valid string encoding
+ fromString() : parse string encoding
* operator << () : regex conform
+ operator == ()
+ operator != ()
* insert() :
+ no duplicated insertions
+ overlap checks
* overlaps() : bugfix of predecessor check
+ shift() : shifts all indices by a given term and creates a new valid list
* CommandLineParsing :
- outNonOverlapping : replaced by outOverlap
- isOutNonOverlapping() : obsolete
- isOutputReportMax() : obsolete
+ outOverlap + validator : overlap encoding
+ getOutputConstraint() : central data structure for output constraints´
- regexRangeEncoding : obsolete due to IndexRangeList::regex
* parseRegion() : now uses IndexRangeList string constructor and shift() for
initialization
* general :
+ E_precisionEpsilon : variable holding the precision epsilon value for
energy equivalence comparisons
* SeedConstraint :
+ range1 + getter : ranges for seed search in seq1
+ range2 + getter : ranges for seed search in seq2
161213 Martin Mann :
* PredictorMfe2d :
* initHybridE :
* code optimizations to reduce lookups
* Predictor* :
+ initOptima()
+ updateOptima()
+ reportOptima()
= generic optima handling
- *Mfe() : replaced by *Optima()
- *MaxPro() : replaced by *Optima()
* IndexRangeList :
+ overlaps( range r ) : whether or not one of the ranges overlaps with r
+ tests
* Predictor* :
* reportOptima( parameters )
* PredictorMfe :
+ reportedInteractions : index range lists to enable non-overlapping
interaction reporting
+ getNextBest() : abstract interface to access the next best non-overlapping
interaction (based on reportedInteractions)
-> implemented by all subclasses
* reportOptima() : now screens for non-overlapping suboptimal interactions
using getNextBest()
161212 Martin Mann :
* InteractionEnergy* :
+ getES*() : ensemble energy of intramolecular substructures within a given
sequence interval under the assumption that the region is part of an
intermolecular multiloop, i.e. contains at least one intramolecular bp
NOTE: not implemented yet, only functions set up
* CommandLineParsing :
+ oNumber + validator : max number of subopts to report
+ oNonOverlapping : whether or not overlapping interactions to report
+ opts_output : new output param category
+ getOutputNumber()
+ isOutputNonOverlapping()
* intaRNA :
+ predict() calls now with getOutputNumber() and isOutputNonOverlapping()
* Interaction :
+ compareEnergy() : checks whether a given interaction has energy higher
than a given value
* operator << (BasePair) now externally defined
* Predictor* :
* predict( + reportMax, + reportNonOverlapping ) : for multi-interaction out
* PredictorMfe :
* initMfe( + reportMax, + reportNonOverlapping ) : for multiple
overlapping interaction reporting
- mfeInteraction : replaced by list of interactions
+ InteractionList : type of double-linked list of interactions
+ mfeInteractions : list of (overlapping) lowest energy interactions
+ traceBack() : now part of abstract interface to be used in reportMfe()
+ reportMfe() : for all interactions from list with E<0: calls traceBack()
and adds to output handler
* updateMfe() :
+ lowest energy interaction list update
+ exclusion of duplicated list insertions (e.g. due to matrix recomputation)
161207 Martin Mann :
* Interaction :
- addInteraction() : obsolete
+ seedRange : optional seed information
+ setSeedRange() : initializes or overwrites seedRange
* PredictorMfe2dSeed :
* PredictorMfe2dHeuristicSeed :
* traceBack() :
+ storing seed interaction information
* OutputHandlerText :
* add() :
+ seed information printed (if available)
+ interaction position printed
+ energy unit added
161120 Martin Mann :
* autotools-init.sh :
* sh -> bash
+ pipefail : script fails on first failed command
* CommandLineParsing :
+ new predictors registered
* default predictor : heuristic
+ time/space infor for each predictor
* bugfix: accessibility length/window check now after individual checks
* Interaction :
+ ostream operator for Interaction::BasePair
* ostream operator uses BasePair operator to reduce redundancy
+ SeedHandler : central handler for seed interaction and access for a given
SeedConstraint
+ fillSeed() : computes the seed information
+ traceBackSeed() : traces a specific seed start
+ getSeedE() : the seed energy for a seed start (or INF if no seed possible)
+ getSeedLength*() : the seed length for a seed start (or 0 if not possible)
* PredictorMfe :
* updateMfe() :
- dangling end based pre-check removed (not sure if valid)
* PredictorMfe2d :
* interface documentation corrected
* PredictorMfe2dSeed :
- seed calculation methods and data structure (move to SeedHandler)
+ seedHandler (generated in constructor)
* fillHybridE_seed() :
* bugfix : init of all cells was not ensured
* sanity checks now include lower i boundary
* PredictorMfe4d : prediction info adapted
+ PredictorMfe2dHeuristic : heuristic mfe prediction in n^2 time and space
+ PredictorMfe2dHeuristicSeed : heuristic mfe prediction in n^2 time and space
including seed constraint
161023 Martin Mann :
* AccessibilityConstraint :
- isBlocked() : renamed to isMarkedBlocked()
* isAccessible() : now : whether or not a position is available for
interaction
+ isMarkedAccessible() : former isAccessible()
+ isMarkedBlocked() : former isBlocked()
* AccessibilityDisabled :
* getED() : checks now for constraint.isAccessible()
* InteractionEnergy :
+ getBasePair() : generates an Interaction BasePair for given indices
+ getIndex*() : generates the computation indices for a given base pair
+ getED*() : fast access to ED of a sequence
+ isAccessible*() : checks for accessibility and non-ambiguity
+ size*() : sequence length
* isValidInteraction() : now protected
* isAllowedLoopRegion() : now protected
+ InteractionEnergyIdxOffset : wrapper for an InteractionEnergy that handles
index shifts due to a given offset. To this end, all according functions are
overwritten, which eases formulations of Predictors.
* Predictor :
* energy : now InteractionEnergyIdxOffset object
* PredictorXXX :
- i*offset : obsolete due to energy class change
* all offsets are now obsolete with extended InteractionEnergy interface and
InteractionEnergyIdxOffset energy access : this simplifies the formulation
of the algorithms and makes debugging easier.
- test/InteractionEnergy_test.cpp : obsolete
161020 Martin Mann :
* configure.ac :
+ boost_regex lib registered
* CommandLineParsing :
+ argument qRegion : query interaction regions (sorted, non-overlapping)
+ argument tRegion : target interaction regions
+ getter and validator
+ regexRangeEncoding : regex to validate range string encodings
+ parseRegion() : parses region argument
* IndexRange :
* constructor() :
* default to = RnaSequence::lastPos
* IndexRangeList :
* push_back() : ascending check corrected
* intaRNA :
+ predicts only for all index range combinations
* ReverseAccessibility :
+ getReversedIndexRange() : reverses an index range
* PredictorMfe2dSeed :
* bugfix : rotating seedE_rec usage not possible; reset to full 5D array
* bugfix : index offset added
161019 Martin Mann :
+ m4/m4_ax_cxx_compile_stdcxx.m4 : enables c11 compiler support check
* configure.ac :
+ ensures c11 compiler compliance via m4_ax_cxx_compile_stdcxx.m4
* defining "_DEBUG" instead of "DEBUG" in debug mode
- enable-c11 flag removed since obsolete (c11 now mandatory)
* .travis : adaption to configure changes
+ easylogging++.h : v9.83 of header-only logging lib (MIT license)
* general.h :
+ includes config.h for configure-based flags
+ IN_DEBUG_MODE : compiler flag to mark debug mode
+ includes easylogging++.h : global logging support
+ easylogging++ log file setup (disabled)
* AccessibilityConstraint :
+ isUnconstrained() : checks whether or not a position is unconstrained
* isBlocked() :
* isAccessible() :
+ quick check for empty list
* AccessibilityVrna :
- log stream : obsolete
* construction :
+ base pair span forwarded to fill* functions
* fillRNAup() also used if sliding window size == 0 (since fastest)
* fill*() :
+ timing added (debug mode only)
+ verbose log of computation mode
* fillByConstraints() :
* getPfScale() :
* fillByRNAup() :
+ uses now base pair span
* CommandLineParsing :
- logStream : obsolete (global logging)
+ seedMaxE argument : maximal overall energy of a seed interaction
+ validate_seedMaxE()
+ seedConstraint : central seed constraint object for all predictors
* getSeedConstraint() : returns constant reference to central object
* InteractionEnergy :
- getInterLoop() : replaced by getInterLeft()
+ getInterLeft() : left side loop extension (former getInterLoop())
+ getPr_danglingLeft() : probability of dangling ends on the left side
+ getPr_danglingRight() : probability of dangling ends on the right side
* getE() :
* getE_contributions() :
* using getPr_dangling*() for dangling end energy computation
* Predictor* :
* predict() :
+ verbose log for prediction mode
+ performance logging in debug mode
* PredictorMfe2dSeed :
* fillSeed() :
+ over energy computation for seed now includes getE_init()
* seed max energy boundary now via SeedConstraint.getMaxE()
* traceBackSeed() :
* bugfix : j2 initialization
* SeedConstraint :
+ maxE + getter : maximal overall energy a seed is allowed to have
161017 Martin Mann :
* CommandLineParsing :
- seedMinBP : renamed to seedBP
- getSeedMinBp : obsolete
+ noSeedRequired : whether or not to enforce seed constraint for interactions
+ seedBP : number of base pairs within seed
+ seedMaxUP : maximal overall number of unpaired bases in seed
+ seedMaxUPq : maximal number of unpaired bases within query's seed
+ seedMaxUPt : maximal number of unpaired bases within target's seed
+ validator_*() for arguments
+ getSeedConstraint() : provides the seed according to the arguments
* parse() :
+ noSeedRequired setup
* getPredictor() : predictor type depends now on noSeedRequired member setup
* general.h :
+ E_isNotINF() : check for energy != E_INF
+ E_isINF() : check for energy == E_INF
* InteractionEnergy :