<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">\r
<toc version="1.0">\r
<tocitem text="Jalview Documentation" target="home" expand="true" >\r
- <tocitem text="What's new" target="new" expand="false">\r
- <tocitem text="EBI Sequence Fetcher" target="seqfetch"/>\r
- <tocitem text="New Output Format Controls" target="preferences"/>\r
- <tocitem text="Enhanced PDB Viewer" target="viewingpdbs"/>\r
- <tocitem text="Sequence Feature Styles" target="seqfeatures"/>\r
- </tocitem>\r
+ <tocitem text="What's new" target="new" expand="false"/>\r
<tocitem text="Release History" target="release"/>\r
- <tocitem text="Alignment Annotations" target ="alannotation"/>\r
- \r
+ <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
+ <tocitem text="Conservation" target="calcs.alconserv"/>\r
+ <tocitem text="Quality" target="calcs.alquality"/>\r
+ </tocitem>\r
<tocitem text="Input / Output" target="io"/>\r
<tocitem text="Key Strokes" target="keys"/>\r
<tocitem text="Making figures" target="export"/>\r
<tocitem text="Editing Alignments" target ="edit"/>\r
+ <tocitem text="Sequence Features" target="seqfeatures"/>\r
<tocitem text="Web Services" target="webservice" expand="false">\r
<tocitem text="Clustal Alignment" target="clustal"/>\r
<tocitem text="Muscle Alignment" target="muscle"/>\r
<tocitem text="User Defined" target="colours.user"/>\r
<tocitem text="Above Percentage Identity" target="colours.abovepid"/>\r
<tocitem text="By conservation" target="colours.conservation"/>\r
+ <tocitem text="By Annotation" target="colours.annotation"/>\r
</tocitem>\r
<tocitem text="Calculations" target="calculations" expand="false">\r
<tocitem text="Sorting alignments" target="sorting"/>\r
<tocitem text="Popup Menu" target="popMenu"/>\r
</tocitem>\r
</tocitem>\r
- <tocitem text="Memory Settings" target="memory"/>\r
+ <tocitem text="Memory Settings" target="memory" expand="false">\r
+ <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>\r
+ </tocitem>\r
</tocitem>\r
<tocitem text="Useful information" expand="true">\r
<tocitem text="Amino Acid Table" target="aminoAcids"/>\r
+ <tocitem text="Amino Acid Properties" target="aaProperties"/>\r
<tocitem text="The Genetic Code" target="geneticCode"/>\r
</tocitem>\r
</toc>\r