build based on 2f9ff46

dev/construction/index.html

@@ -127,4 +127,4 @@
 (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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Thursday 22 June 2023 14:01">Thursday 22 June 2023</span>. Using Julia version 1.9.1.</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="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 0.27.25 on <span class="colophon-date" title="Monday 21 August 2023 07:06">Monday 21 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/counting/index.html

@@ -6,4 +6,4 @@
 
 julia> count(==, dna"ATCGM", dna"GCCGM")
 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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Thursday 22 June 2023 14:01">Thursday 22 June 2023</span>. Using Julia version 1.9.1.</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 21 August 2023 07:06">Monday 21 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>