build based on 457e9b7

Author: Documenter.jl

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-09T22:42:07","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-02T03:53:50","documenter_version":"1.6.0"}}

dev/api/index.html

@@ -117,4 +117,4 @@
 
 axislegend(ax)
 
-f</code></pre><p><img src="../assets/lors-lambda.png" alt/></p><p>What this plot shows is that the ORFs in the lambda genome have a higher scores than random sequences of the same length. The score is a measure of how likely a sequence given the coding model is compared to the non-coding model. In other words, the higher the score the more likely the sequence is coding. So, the plot shows that the ORFs in the lambda genome are more likely to be coding regions than random sequences. It also shows that the longer the ORFI the higher the score, which is expected since longer ORFs are more likely to be coding regions than shorter ones.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../naivefinder/">« Finding ORFs</a><a class="docs-footer-nextpage" href="../simplecodingrule/">A Simple Coding Rule »</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 1.5.0 on <span class="colophon-date" title="Friday 9 August 2024 22:42">Friday 9 August 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+f</code></pre><p><img src="../assets/lors-lambda.png" alt/></p><p>What this plot shows is that the ORFs in the lambda genome have a higher scores than random sequences of the same length. The score is a measure of how likely a sequence given the coding model is compared to the non-coding model. In other words, the higher the score the more likely the sequence is coding. So, the plot shows that the ORFs in the lambda genome are more likely to be coding regions than random sequences. It also shows that the longer the ORFI the higher the score, which is expected since longer ORFs are more likely to be coding regions than shorter ones.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../naivefinder/">« Finding ORFs</a><a class="docs-footer-nextpage" href="../simplecodingrule/">A Simple Coding Rule »</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 1.6.0 on <span class="colophon-date" title="Monday 2 September 2024 03:53">Monday 2 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/assets/documenter.js

@@ -41,4 +41,4 @@
 	version = {v0.6.0},
 	year    = {2024},
 	month   = {08}
-}</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="naivefinder/">Finding ORFs »</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 1.5.0 on <span class="colophon-date" title="Friday 9 August 2024 22:42">Friday 9 August 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+}</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="naivefinder/">Finding ORFs »</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 1.6.0 on <span class="colophon-date" title="Monday 2 September 2024 03:53">Monday 2 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/features/index.html

@@ -31,4 +31,4 @@
 >seq id=11 start=581 stop=601 strand=+ frame=2 features=[]
 ATGTGTCCAACGGCAGCCTGA
 >seq id=12 start=695 stop=706 strand=+ frame=2 features=[]
-ATGCAACCCTGA</code></pre><p>This could also be done to writting a <code>FASTA</code> file with the nucleotide sequences of the ORFIs using the <code>write_orfs_fna</code> function. Similarly for the <code>BED</code> and <code>GFF</code> files using the <code>write_orfs_bed</code> and <code>write_orfs_gff</code> functions respectively.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../simplecodingrule/">« A Simple Coding Rule</a><a class="docs-footer-nextpage" href="../api/">API »</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 1.5.0 on <span class="colophon-date" title="Friday 9 August 2024 22:42">Friday 9 August 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ATGCAACCCTGA</code></pre><p>This could also be done to writting a <code>FASTA</code> file with the nucleotide sequences of the ORFIs using the <code>write_orfs_fna</code> function. Similarly for the <code>BED</code> and <code>GFF</code> files using the <code>write_orfs_bed</code> and <code>write_orfs_gff</code> functions respectively.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../simplecodingrule/">« A Simple Coding Rule</a><a class="docs-footer-nextpage" href="../api/">API »</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 1.6.0 on <span class="colophon-date" title="Monday 2 September 2024 03:53">Monday 2 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/index.html

@@ -56,4 +56,4 @@
  MSPHKAM*
  M*
  MCPTAA*
- MQP*</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../features/">Scoring ORFs »</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 1.5.0 on <span class="colophon-date" title="Friday 9 August 2024 22:42">Friday 9 August 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ MQP*</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../features/">Scoring ORFs »</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 1.6.0 on <span class="colophon-date" title="Monday 2 September 2024 03:53">Monday 2 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>