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Documenter.jl committed Sep 26, 2023
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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-09-26T11:19:56","documenter_version":"1.0.1"}}
{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-09-26T11:27:40","documenter_version":"1.0.1"}}
2 changes: 1 addition & 1 deletion dev/construction/index.html
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(false, false)

julia> length(seq) == length(vec) && 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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.0.1 on <span class="colophon-date" title="Tuesday 26 September 2023 11:19">Tuesday 26 September 2023</span>. Using Julia version 1.9.3.</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.0.1 on <span class="colophon-date" title="Tuesday 26 September 2023 11:27">Tuesday 26 September 2023</span>. Using Julia version 1.9.3.</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="../iteration/">« Iteration</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.0.1 on <span class="colophon-date" title="Tuesday 26 September 2023 11:19">Tuesday 26 September 2023</span>. Using Julia version 1.9.3.</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="../iteration/">« Iteration</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.0.1 on <span class="colophon-date" title="Tuesday 26 September 2023 11:27">Tuesday 26 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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