build based on e9633fc

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-28T10:50:11","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-28T10:50:59","documenter_version":"1.4.1"}}

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/18d70d5b75da94913ea59dfa9570b6ff69c9effb/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></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/e9633fcfde0cd92122a1a76cf755f13f10ab76b7/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></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/18d70d5b75da94913ea59dfa9570b6ff69c9effb/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></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/e9633fcfde0cd92122a1a76cf755f13f10ab76b7/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></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/18d70d5b75da94913ea59dfa9570b6ff69c9effb/src/longsequences/stringliterals.jl#L89-L100">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);
+PKLEQC</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/e9633fcfde0cd92122a1a76cf755f13f10ab76b7/src/longsequences/stringliterals.jl#L89-L100">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)

dev/interfaces/index.html

@@ -59,4 +59,4 @@
 julia> Base.copy(seq::Codon) = Codon(seq.x)
 
 julia> BioSequences.has_interface(BioSequence, Codon, [RNA_C, RNA_U, RNA_A], false)
-true</code></pre><h2 id="Interface-checking-functions"><a class="docs-heading-anchor" href="#Interface-checking-functions">Interface checking functions</a><a id="Interface-checking-functions-1"></a><a class="docs-heading-anchor-permalink" href="#Interface-checking-functions" title="Permalink"></a></h2><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.has_interface" href="#BioSequences.has_interface"><code>BioSequences.has_interface</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">function has_interface(::Type{Alphabet}, A::Alphabet)</code></pre><p>Returns whether <code>A</code> conforms to the <code>Alphabet</code> interface.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/18d70d5b75da94913ea59dfa9570b6ff69c9effb/src/alphabet.jl#L41-L45">source</a></section><section><div><pre><code class="language-julia hljs">has_interface(::Type{BioSequence}, ::T, syms::Vector, mutable::Bool, compat::Bool=true)</code></pre><p>Check if type <code>T</code> conforms to the <code>BioSequence</code> interface. A <code>T</code> is constructed from the vector of element types <code>syms</code> which must not be empty. If the <code>mutable</code> flag is set, also check the mutable interface. If the <code>compat</code> flag is set, check for compatibility with existing alphabets.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/18d70d5b75da94913ea59dfa9570b6ff69c9effb/src/biosequence/biosequence.jl#L44-L51">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../io/">« I/O</a><a class="docs-footer-nextpage" href="../recipes/">Recipes »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Tuesday 28 May 2024 10:50">Tuesday 28 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+true</code></pre><h2 id="Interface-checking-functions"><a class="docs-heading-anchor" href="#Interface-checking-functions">Interface checking functions</a><a id="Interface-checking-functions-1"></a><a class="docs-heading-anchor-permalink" href="#Interface-checking-functions" title="Permalink"></a></h2><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.has_interface" href="#BioSequences.has_interface"><code>BioSequences.has_interface</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">function has_interface(::Type{Alphabet}, A::Alphabet)</code></pre><p>Returns whether <code>A</code> conforms to the <code>Alphabet</code> interface.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/e9633fcfde0cd92122a1a76cf755f13f10ab76b7/src/alphabet.jl#L41-L45">source</a></section><section><div><pre><code class="language-julia hljs">has_interface(::Type{BioSequence}, ::T, syms::Vector, mutable::Bool, compat::Bool=true)</code></pre><p>Check if type <code>T</code> conforms to the <code>BioSequence</code> interface. A <code>T</code> is constructed from the vector of element types <code>syms</code> which must not be empty. If the <code>mutable</code> flag is set, also check the mutable interface. If the <code>compat</code> flag is set, check for compatibility with existing alphabets.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioSequences.jl/blob/e9633fcfde0cd92122a1a76cf755f13f10ab76b7/src/biosequence/biosequence.jl#L44-L51">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../io/">« I/O</a><a class="docs-footer-nextpage" href="../recipes/">Recipes »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Tuesday 28 May 2024 10:50">Tuesday 28 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>