Skip to content

Commit

Permalink
build based on bfcc1b1
Browse files Browse the repository at this point in the history
  • Loading branch information
Documenter.jl committed Nov 12, 2024
1 parent b56e56b commit 1de7c8c
Show file tree
Hide file tree
Showing 8 changed files with 13 additions and 13 deletions.
2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-12T13:04:49","documenter_version":"1.7.0"}}
{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-12T13:17:43","documenter_version":"1.7.0"}}
8 changes: 4 additions & 4 deletions dev/accessing/index.html
View file

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion dev/examples/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,4 +30,4 @@
for chr in chrs
write(w, chr)
end
end</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../genes/">« Filtering: the @genes macro</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 12 November 2024 13:04">Tuesday 12 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
end</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../genes/">« Filtering: the @genes macro</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 12 November 2024 13:17">Tuesday 12 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/genes/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,4 +28,4 @@
@genes(chr, :locus_tag in d[$:category1])

gene = chr.genes[5]
@genes(chr, gene == $gene)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/a36bb21b510ef63d52969ae809277116cf3abdf9/src/macro.jl#L68-L126">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../loci/">« Representing genomic loci</a><a class="docs-footer-nextpage" href="../examples/">Examples »</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 12 November 2024 13:04">Tuesday 12 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
@genes(chr, gene == $gene)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/bfcc1b1fc3b738ac7ab816d6a6effa1243f18df0/src/macro.jl#L68-L126">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../loci/">« Representing genomic loci</a><a class="docs-footer-nextpage" href="../examples/">Examples »</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 12 November 2024 13:17">Tuesday 12 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -39,4 +39,4 @@

open(GenBank.Writer, &quot;updated.gbk&quot;) do w
write(w, chr)
end</code></pre></article><nav class="docs-footer"><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><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 12 November 2024 13:04">Tuesday 12 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
end</code></pre></article><nav class="docs-footer"><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><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 12 November 2024 13:17">Tuesday 12 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
6 changes: 3 additions & 3 deletions dev/io/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@
for record in record
print(record)
end
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/a36bb21b510ef63d52969ae809277116cf3abdf9/src/GenBank/reader.jl#L7-L19">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="GenomicAnnotations.GFF.Reader" href="#GenomicAnnotations.GFF.Reader"><code>GenomicAnnotations.GFF.Reader</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GFF.Reader(input::IO)</code></pre><p>Create a data reader of the GFF3 file format.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/a36bb21b510ef63d52969ae809277116cf3abdf9/src/GFF/reader.jl#L7-L11">source</a></section></article><h2 id="Output"><a class="docs-heading-anchor" href="#Output">Output</a><a id="Output-1"></a><a class="docs-heading-anchor-permalink" href="#Output" title="Permalink"></a></h2><p>Annotations can be printed with GenBank formatting using <code>GenBank.Writer</code>, and as GFF3 with <code>GFF.Writer</code>. Headers are not automatically converted between formats; <code>GFF.Writer</code> only prints the header of the first <code>Record</code>, and only if it starts with a <code>#</code>, while <code>GenBank.Writer</code> prints a default header if the stored one starts with <code>#</code>.</p><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="GenomicAnnotations.GenBank.Writer" href="#GenomicAnnotations.GenBank.Writer"><code>GenomicAnnotations.GenBank.Writer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GenBank.Writer(output::IO; width=70)</code></pre><p>Create a data writer of the GenBank file format.</p><pre><code class="language-julia hljs">open(GenBank.Writer, outfile) do writer
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/bfcc1b1fc3b738ac7ab816d6a6effa1243f18df0/src/GenBank/reader.jl#L7-L19">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="GenomicAnnotations.GFF.Reader" href="#GenomicAnnotations.GFF.Reader"><code>GenomicAnnotations.GFF.Reader</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GFF.Reader(input::IO)</code></pre><p>Create a data reader of the GFF3 file format.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/bfcc1b1fc3b738ac7ab816d6a6effa1243f18df0/src/GFF/reader.jl#L7-L11">source</a></section></article><h2 id="Output"><a class="docs-heading-anchor" href="#Output">Output</a><a id="Output-1"></a><a class="docs-heading-anchor-permalink" href="#Output" title="Permalink"></a></h2><p>Annotations can be printed with GenBank formatting using <code>GenBank.Writer</code>, and as GFF3 with <code>GFF.Writer</code>. Headers are not automatically converted between formats; <code>GFF.Writer</code> only prints the header of the first <code>Record</code>, and only if it starts with a <code>#</code>, while <code>GenBank.Writer</code> prints a default header if the stored one starts with <code>#</code>.</p><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="GenomicAnnotations.GenBank.Writer" href="#GenomicAnnotations.GenBank.Writer"><code>GenomicAnnotations.GenBank.Writer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GenBank.Writer(output::IO; width=70)</code></pre><p>Create a data writer of the GenBank file format.</p><pre><code class="language-julia hljs">open(GenBank.Writer, outfile) do writer
write(writer, genome)
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/a36bb21b510ef63d52969ae809277116cf3abdf9/src/GenBank/writer.jl#L11-L20">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="GenomicAnnotations.GFF.Writer" href="#GenomicAnnotations.GFF.Writer"><code>GenomicAnnotations.GFF.Writer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GFF.Writer(output::IO; width=70)</code></pre><p>Create a data writer of the GFF file format.</p><pre><code class="language-julia hljs">open(GFF.Writer, outfile) do writer
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/bfcc1b1fc3b738ac7ab816d6a6effa1243f18df0/src/GenBank/writer.jl#L11-L20">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="GenomicAnnotations.GFF.Writer" href="#GenomicAnnotations.GFF.Writer"><code>GenomicAnnotations.GFF.Writer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GFF.Writer(output::IO; width=70)</code></pre><p>Create a data writer of the GFF file format.</p><pre><code class="language-julia hljs">open(GFF.Writer, outfile) do writer
write(writer, genome)
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/a36bb21b510ef63d52969ae809277116cf3abdf9/src/GFF/writer.jl#L11-L20">source</a></section></article><p>In the REPL, instances of <code>Gene</code> are displayed as they would be in the annotation file.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« GenomicAnnotations.jl</a><a class="docs-footer-nextpage" href="../accessing/">Accessing and modifying annotations »</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 12 November 2024 13:04">Tuesday 12 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/bfcc1b1fc3b738ac7ab816d6a6effa1243f18df0/src/GFF/writer.jl#L11-L20">source</a></section></article><p>In the REPL, instances of <code>Gene</code> are displayed as they would be in the annotation file.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« GenomicAnnotations.jl</a><a class="docs-footer-nextpage" href="../accessing/">Accessing and modifying annotations »</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 12 November 2024 13:17">Tuesday 12 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
Loading

0 comments on commit 1de7c8c

Please sign in to comment.