build based on 2933ffb

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-10-22T12:34:42","documenter_version":"1.7.0"}}
+{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-10-22T16:18:36","documenter_version":"1.7.0"}}

dev/construction/index.html

@@ -135,11 +135,11 @@
 "TAGA"
 
 julia> string(push!(f(), DNA_A))
-&quot;TAGA&quot;</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/b47c3d62e7e4405221b3d5535d426d237e43ce06/src/longsequences/stringliterals.jl#L12-L45">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="BioSequences.@rna_str" href="#BioSequences.@rna_str"><code>BioSequences.@rna_str</code></a> — <span class="docstring-category">Macro</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><p>The <code>LongRNA{4}</code> equivalent to <code>@dna_str</code></p><p>See also: <a href="#BioSequences.@dna_str"><code>@dna_str</code></a>, <a href="#BioSequences.@aa_str"><code>@aa_str</code></a></p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; rna&quot;UCGUGAUGC&quot;
+&quot;TAGA&quot;</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/2933ffbb7486393e76500ac0f3a63027074be418/src/longsequences/stringliterals.jl#L12-L45">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="BioSequences.@rna_str" href="#BioSequences.@rna_str"><code>BioSequences.@rna_str</code></a> — <span class="docstring-category">Macro</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><p>The <code>LongRNA{4}</code> equivalent to <code>@dna_str</code></p><p>See also: <a href="#BioSequences.@dna_str"><code>@dna_str</code></a>, <a href="#BioSequences.@aa_str"><code>@aa_str</code></a></p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; rna&quot;UCGUGAUGC&quot;
 9nt RNA Sequence:
-UCGUGAUGC</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/b47c3d62e7e4405221b3d5535d426d237e43ce06/src/longsequences/stringliterals.jl#L61-L72">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="BioSequences.@aa_str" href="#BioSequences.@aa_str"><code>BioSequences.@aa_str</code></a> — <span class="docstring-category">Macro</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><p>The <code>AminoAcidAlphabet</code> equivalent to <code>@dna_str</code></p><p>See also: <a href="#BioSequences.@dna_str"><code>@dna_str</code></a>, <a href="#BioSequences.@rna_str"><code>@rna_str</code></a></p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; aa&quot;PKLEQC&quot;
+UCGUGAUGC</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/2933ffbb7486393e76500ac0f3a63027074be418/src/longsequences/stringliterals.jl#L61-L72">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="BioSequences.@aa_str" href="#BioSequences.@aa_str"><code>BioSequences.@aa_str</code></a> — <span class="docstring-category">Macro</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><p>The <code>AminoAcidAlphabet</code> equivalent to <code>@dna_str</code></p><p>See also: <a href="#BioSequences.@dna_str"><code>@dna_str</code></a>, <a href="#BioSequences.@rna_str"><code>@rna_str</code></a></p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; aa&quot;PKLEQC&quot;
 6aa Amino Acid Sequence:
-PKLEQC</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/b47c3d62e7e4405221b3d5535d426d237e43ce06/src/longsequences/stringliterals.jl#L89-L100">source</a></section></article><h2 id="Loose-parsing"><a class="docs-heading-anchor" href="#Loose-parsing">Loose parsing</a><a id="Loose-parsing-1"></a><a class="docs-heading-anchor-permalink" href="#Loose-parsing" title="Permalink"></a></h2><p>As of version 3.2.0, BioSequences.jl provide the <a href="#BioSequences.bioseq"><code>bioseq</code></a> function, which can be used to build a <code>LongSequence</code> from a string (or an <code>AbstractVector{UInt8}</code>) without knowing the correct <code>Alphabet</code>.</p><pre><code class="language-julia-repl hljs">julia&gt; bioseq(&quot;ATGTGCTGA&quot;)
+PKLEQC</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/2933ffbb7486393e76500ac0f3a63027074be418/src/longsequences/stringliterals.jl#L89-L100">source</a></section></article><h2 id="Loose-parsing"><a class="docs-heading-anchor" href="#Loose-parsing">Loose parsing</a><a id="Loose-parsing-1"></a><a class="docs-heading-anchor-permalink" href="#Loose-parsing" title="Permalink"></a></h2><p>As of version 3.2.0, BioSequences.jl provide the <a href="#BioSequences.bioseq"><code>bioseq</code></a> function, which can be used to build a <code>LongSequence</code> from a string (or an <code>AbstractVector{UInt8}</code>) without knowing the correct <code>Alphabet</code>.</p><pre><code class="language-julia-repl hljs">julia&gt; bioseq(&quot;ATGTGCTGA&quot;)
 9nt DNA Sequence:
 ATGTGCTGA</code></pre><p>The function will prioritise 2-bit alphabets over 4-bit alphabets, and prefer smaller alphabets (like <code>DNAAlphabet{4}</code>) over larger (like <code>AminoAcidAlphabet</code>). If the input cannot be encoded by any of the built-in alphabets, an error is thrown:</p><pre><code class="language-julia-repl hljs">julia&gt; bioseq(&quot;0!(CC!;#&amp;&amp;%&quot;)
 ERROR: cannot encode 0x30 in AminoAcidAlphabet
@@ -153,7 +153,7 @@
 
 julia&gt; bioseq(&quot;PKMW#3&gt;&gt;0;kL&quot;)
 ERROR: cannot encode 0x23 in AminoAcidAlphabet
-[...]</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/b47c3d62e7e4405221b3d5535d426d237e43ce06/src/longsequences/constructors.jl#L90-L116">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="BioSequences.guess_alphabet" href="#BioSequences.guess_alphabet"><code>BioSequences.guess_alphabet</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">guess_alphabet(s::Union{AbstractString, AbstractVector{UInt8}}) -&gt; Union{Integer, Alphabet}</code></pre><p>Pick an <code>Alphabet</code> that can encode input <code>s</code>.  If no <code>Alphabet</code> can, return the index of the first byte of the input which is not encodable in any alphabet. This function only knows about the alphabets listed below. If multiple alphabets are possible, pick the first from the order below (i.e. <code>DNAAlphabet{2}()</code> if possible, otherwise <code>RNAAlphabet{2}()</code> etc).</p><ol><li><code>DNAAlphabet{2}()</code></li><li><code>RNAAlphabet{2}()</code></li><li><code>DNAAlphabet{4}()</code></li><li><code>RNAAlphabet{4}()</code></li><li><code>AminoAcidAlphabet()</code></li></ol><div class="admonition is-warning"><header class="admonition-header">Warning</header><div class="admonition-body"><p>The functions <code>bioseq</code> and <code>guess_alphabet</code> are intended for use in interactive sessions, and are not suitable for use in packages or non-ephemeral work. They are type unstable, and their heuristics <strong>are subject to change</strong> in minor versions.</p></div></div><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; guess_alphabet(&quot;AGGCA&quot;)
+[...]</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/2933ffbb7486393e76500ac0f3a63027074be418/src/longsequences/constructors.jl#L90-L116">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="BioSequences.guess_alphabet" href="#BioSequences.guess_alphabet"><code>BioSequences.guess_alphabet</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">guess_alphabet(s::Union{AbstractString, AbstractVector{UInt8}}) -&gt; Union{Integer, Alphabet}</code></pre><p>Pick an <code>Alphabet</code> that can encode input <code>s</code>.  If no <code>Alphabet</code> can, return the index of the first byte of the input which is not encodable in any alphabet. This function only knows about the alphabets listed below. If multiple alphabets are possible, pick the first from the order below (i.e. <code>DNAAlphabet{2}()</code> if possible, otherwise <code>RNAAlphabet{2}()</code> etc).</p><ol><li><code>DNAAlphabet{2}()</code></li><li><code>RNAAlphabet{2}()</code></li><li><code>DNAAlphabet{4}()</code></li><li><code>RNAAlphabet{4}()</code></li><li><code>AminoAcidAlphabet()</code></li></ol><div class="admonition is-warning"><header class="admonition-header">Warning</header><div class="admonition-body"><p>The functions <code>bioseq</code> and <code>guess_alphabet</code> are intended for use in interactive sessions, and are not suitable for use in packages or non-ephemeral work. They are type unstable, and their heuristics <strong>are subject to change</strong> in minor versions.</p></div></div><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; guess_alphabet(&quot;AGGCA&quot;)
 DNAAlphabet{2}()
 
 julia&gt; guess_alphabet(&quot;WKLQSTV&quot;)
@@ -163,10 +163,10 @@
 5
 
 julia&gt; guess_alphabet(&quot;UAGCSKMU&quot;)
-RNAAlphabet{4}()</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/b47c3d62e7e4405221b3d5535d426d237e43ce06/src/alphabet.jl#L328-L360">source</a></section></article><h2 id="Comparison-to-other-sequence-types"><a class="docs-heading-anchor" href="#Comparison-to-other-sequence-types">Comparison to other sequence types</a><a id="Comparison-to-other-sequence-types-1"></a><a class="docs-heading-anchor-permalink" href="#Comparison-to-other-sequence-types" title="Permalink"></a></h2><p>Following Base standards, BioSequences do not compare equal to other containers even if they have the same elements. To e.g. compare a BioSequence with a vector of DNA, compare the elements themselves:</p><pre><code class="language-julia-repl hljs">julia&gt; seq = dna&quot;GAGCTGA&quot;; vec = collect(seq);
+RNAAlphabet{4}()</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/2933ffbb7486393e76500ac0f3a63027074be418/src/alphabet.jl#L328-L360">source</a></section></article><h2 id="Comparison-to-other-sequence-types"><a class="docs-heading-anchor" href="#Comparison-to-other-sequence-types">Comparison to other sequence types</a><a id="Comparison-to-other-sequence-types-1"></a><a class="docs-heading-anchor-permalink" href="#Comparison-to-other-sequence-types" title="Permalink"></a></h2><p>Following Base standards, BioSequences do not compare equal to other containers even if they have the same elements. To e.g. compare a BioSequence with a vector of DNA, compare the elements themselves:</p><pre><code class="language-julia-repl hljs">julia&gt; seq = dna&quot;GAGCTGA&quot;; vec = collect(seq);
 
 julia&gt; seq == vec, isequal(seq, vec)
 (false, false)
 
 julia&gt; length(seq) == length(vec) &amp;&amp; all(i == j for (i, j) in zip(seq, vec))
-true </code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../types/">« BioSequences Types</a><a class="docs-footer-nextpage" href="../transforms/">Indexing &amp; modifying sequences »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Tuesday 22 October 2024 12:34">Tuesday 22 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+true </code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../types/">« BioSequences Types</a><a class="docs-footer-nextpage" href="../transforms/">Indexing &amp; modifying sequences »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Tuesday 22 October 2024 16:18">Tuesday 22 October 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>