<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
- <tocitem text="Retrieval from ENSEMBL" target="ensemblfetch" />
- <tocitem text="UniProt Free Text Search" target="uniprotfetcher" />
- <tocitem text="SIFTS for mapping PDB structures to UniProt" target="siftsmapping" />
<tocitem text="Latest Release Notes" target="release"/>
+ <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+ <tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
+ <tocitem text="Omit hidden regions in Overview" target="overview"/>
+ <tocitem text="identifers.org for URL Links" target="linksprefs" />
+ <tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
<tocitem text="Sequence Alignment" target="msaservice" expand="false">
<tocitem text="Multiple Alignment Subjobs" target="msaservice" />
</tocitem>
- <tocitem text="Secondary Structure Prediction" target="jnet" />
+ <tocitem text="Secondary Structure Prediction" target="jpred" />
<tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
<tocitem text="Protein Disorder Prediction" target="disorder" />
<tocitem text="Alignment Conservation Analysis" target="aacon" />
<tocitem text="Chimera Viewer" target="chimera" />
</tocitem>
<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
+ <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
+ <tocitem text="Configuring URL Links" target="linksprefs" />
+ </tocitem>
<tocitem text="VAMSAS Data Exchange" target="vamsas">
<!-- what can Jalview share with other apps -->
<!-- what other apps exist -->
<tocitem text="Preferences" target="preferences" />
<tocitem text="Memory Settings" target="memory" expand="false"/>
<tocitem text="Scripting with Groovy" target="groovy">
- <tocitem text="Groovy Feature Counter example" target="groovy.featurecounter"/>
+ <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
</tocitem>
<tocitem text="Command Line" target="commandline" expand="false">
<tocitem text="Command Line Arguments" target="clarguments" />