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Documenter.jl committed Jun 24, 2024
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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-24T12:35:17","documenter_version":"1.4.1"}}
{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-24T14:48:43","documenter_version":"1.4.1"}}
8 changes: 4 additions & 4 deletions dev/construction/index.html
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"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/db4be03de5a75ace22ec87e84288ed96e97faf1a/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/cbb5397e747bae9138a4f86989e5fcc5a1fbd826/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/db4be03de5a75ace22ec87e84288ed96e97faf1a/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/cbb5397e747bae9138a4f86989e5fcc5a1fbd826/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/db4be03de5a75ace22ec87e84288ed96e97faf1a/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/cbb5397e747bae9138a4f86989e5fcc5a1fbd826/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)

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></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="Monday 24 June 2024 12:35">Monday 24 June 2024</span>. Using Julia version 1.10.4.</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></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="Monday 24 June 2024 14:48">Monday 24 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/counting/index.html
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julia&gt; count(==, dna&quot;ATCGM&quot;, dna&quot;GCCGM&quot;)
3
</code></pre><h2 id="Alias-functions"><a class="docs-heading-anchor" href="#Alias-functions">Alias functions</a><a id="Alias-functions-1"></a><a class="docs-heading-anchor-permalink" href="#Alias-functions" title="Permalink"></a></h2><p>A number of functions which are aliases for various invocations of <code>Base.count</code> are provided.</p><table><tr><th style="text-align: left">Alias function</th><th style="text-align: left">Base.count call(s)</th></tr><tr><td style="text-align: left"><code>n_ambiguous</code></td><td style="text-align: left"><code>count(isambiguous, seq)</code>, <code>count(isambiguous, seqa, seqb)</code></td></tr><tr><td style="text-align: left"><code>n_certain</code></td><td style="text-align: left"><code>count(iscertain, seq)</code>, <code>count(iscertain, seqa, seqb)</code></td></tr><tr><td style="text-align: left"><code>n_gap</code></td><td style="text-align: left"><code>count(isgap, seq)</code>, <code>count(isgap, seqa, seqb)</code></td></tr><tr><td style="text-align: left"><code>matches</code></td><td style="text-align: left"><code>count(==, seqa, seqb)</code></td></tr><tr><td style="text-align: left"><code>mismatches</code></td><td style="text-align: left"><code>count(!=, seqa, seqb)</code></td></tr></table><h2 id="Bit-parallel-optimisations"><a class="docs-heading-anchor" href="#Bit-parallel-optimisations">Bit-parallel optimisations</a><a id="Bit-parallel-optimisations-1"></a><a class="docs-heading-anchor-permalink" href="#Bit-parallel-optimisations" title="Permalink"></a></h2><p>For the vast majority of <code>Base.count(f, seq)</code> and <code>Base.count(f, seqa, seqb)</code> methods, a naive counting is done: the internal <code>count_naive</code> function is called, which simply loops over each position, applies <code>f</code>, and accumulates the result.</p><p>However, for some functions, it is possible to implement highly efficient methods that use bit-parallelism to check many elements at one time. This is made possible by the succinct encoding of BioSequences. Usually <code>f</code> is one of the functions provided by BioSymbols.jl or by BioSequences.jl</p><p>For such sequence and function combinations, <code>Base.count(f, seq)</code> is overloaded to call an internal <code>BioSequences.count_*_bitpar</code> function, which is passed the sequence(s). If you want to force BioSequences to use naive counting for the purposes of testing or debugging for example, then you can call <code>BioSequences.count_naive</code> directly.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../sequence_search/">« Pattern matching and searching</a><a class="docs-footer-nextpage" href="../io/">I/O »</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="Monday 24 June 2024 12:35">Monday 24 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
</code></pre><h2 id="Alias-functions"><a class="docs-heading-anchor" href="#Alias-functions">Alias functions</a><a id="Alias-functions-1"></a><a class="docs-heading-anchor-permalink" href="#Alias-functions" title="Permalink"></a></h2><p>A number of functions which are aliases for various invocations of <code>Base.count</code> are provided.</p><table><tr><th style="text-align: left">Alias function</th><th style="text-align: left">Base.count call(s)</th></tr><tr><td style="text-align: left"><code>n_ambiguous</code></td><td style="text-align: left"><code>count(isambiguous, seq)</code>, <code>count(isambiguous, seqa, seqb)</code></td></tr><tr><td style="text-align: left"><code>n_certain</code></td><td style="text-align: left"><code>count(iscertain, seq)</code>, <code>count(iscertain, seqa, seqb)</code></td></tr><tr><td style="text-align: left"><code>n_gap</code></td><td style="text-align: left"><code>count(isgap, seq)</code>, <code>count(isgap, seqa, seqb)</code></td></tr><tr><td style="text-align: left"><code>matches</code></td><td style="text-align: left"><code>count(==, seqa, seqb)</code></td></tr><tr><td style="text-align: left"><code>mismatches</code></td><td style="text-align: left"><code>count(!=, seqa, seqb)</code></td></tr></table><h2 id="Bit-parallel-optimisations"><a class="docs-heading-anchor" href="#Bit-parallel-optimisations">Bit-parallel optimisations</a><a id="Bit-parallel-optimisations-1"></a><a class="docs-heading-anchor-permalink" href="#Bit-parallel-optimisations" title="Permalink"></a></h2><p>For the vast majority of <code>Base.count(f, seq)</code> and <code>Base.count(f, seqa, seqb)</code> methods, a naive counting is done: the internal <code>count_naive</code> function is called, which simply loops over each position, applies <code>f</code>, and accumulates the result.</p><p>However, for some functions, it is possible to implement highly efficient methods that use bit-parallelism to check many elements at one time. This is made possible by the succinct encoding of BioSequences. Usually <code>f</code> is one of the functions provided by BioSymbols.jl or by BioSequences.jl</p><p>For such sequence and function combinations, <code>Base.count(f, seq)</code> is overloaded to call an internal <code>BioSequences.count_*_bitpar</code> function, which is passed the sequence(s). If you want to force BioSequences to use naive counting for the purposes of testing or debugging for example, then you can call <code>BioSequences.count_naive</code> directly.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../sequence_search/">« Pattern matching and searching</a><a class="docs-footer-nextpage" href="../io/">I/O »</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="Monday 24 June 2024 14:48">Monday 24 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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