+++ /dev/null
-<?xml version="1.0" encoding="ISO-8859-1" ?>
-<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
-<toc version="1.0">
-<tocitem text="Jalview Documentation" target="home" expand="true" >
- <tocitem text="What's new" target="new" expand="true">
- <tocitem text="Release History" target="release"/>
- <tocitem text="Mapping between Sequences" target="seqmappings"/>
- <tocitem text="Coding Region Sequence Features" target="cdnafeatures"/>
- </tocitem>
- <tocitem text="Editing Alignments" target ="edit"/>
- <tocitem text="Cursor Mode" target="cursor"/>
- <tocitem text="Key Strokes" target="keys"/>
- <tocitem text="Input / Output" target="io"/>
- <tocitem text="Making figures" target="export"/>
- <tocitem text="Hidden Regions" target="hiddenRegions"/>
- <tocitem text="Viewing PDB Files" target="viewingpdbs"/>
- <tocitem text="Multiple Views" target="multipleviews"/>
- <tocitem text="Sequence Features" target="seqfeatures" expand="false">
- <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
- <tocitem text="Sequence Features File" target="features.fileformat"/>
- <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
- <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
- <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
- <tocitem text="DAS Feature Settings" target="das.settings"/>
- </tocitem>
- <tocitem text="Web Services" target="webservice" expand="false">
- <tocitem text="Sequence Alignment" target="msaservice" expand="false">
- <tocitem text="Clustal Alignment" target="clustal"/>
- <tocitem text="Muscle Alignment" target="muscle"/>
- <tocitem text="MAFFT Alignment" target="mafft"/>
- <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
- </tocitem>
- <tocitem text="Secondary Structure Prediction" target="jnet"/>
- </tocitem>
- <tocitem text="Colour Schemes" target="colours" expand="false">
- <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
- <tocitem text="ClustalX" target="colours.clustal"/>
- <tocitem text="Zappo" target="colours.zappo"/>
- <tocitem text="Taylor" target="colours.taylor"/>
- <tocitem text="Hydrophobicity" target="colours.hydro"/>
- <tocitem text="Helix propensity" target="colours.helix"/>
- <tocitem text="Strand propensity" target="colours.strand"/>
- <tocitem text="Turn propensity" target="colours.turn"/>
- <tocitem text="Buried index" target="colours.buried"/>
- <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
- <tocitem text="Blosum62" target="colours.blosum"/>
- <tocitem text="by Percentage Identity" target="colours.pid"/>
- <tocitem text="User Defined" target="colours.user"/>
- <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
- <tocitem text="By conservation" target="colours.conservation"/>
- <tocitem text="By Annotation" target="colours.annotation"/>
- </tocitem>
- <tocitem text="Calculations" target="calculations" expand="false">
- <tocitem text="Sorting alignments" target="sorting"/>
- <tocitem text="Calculating trees" target="trees"/>
- <tocitem text="Principal Component Analysis" target="pca"/>
- <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
- <tocitem text="Pairwise Alignments" target="pairwise"/>
- <tocitem text="Remove Redundancy" target="redundancy"/>
- </tocitem>
- <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
- <tocitem text="Conservation" target="calcs.alconserv"/>
- <tocitem text="Quality" target="calcs.alquality"/>
- <tocitem text="Consensus" target="calcs.consensus"/>
- <tocitem text="Annotations File Format" target="annotations.fileformat"/>
- </tocitem>
- <tocitem text="Window Menus" target="menus" expand="false">
- <tocitem text="Desktop Window" target="desktopMenu"/>
- <tocitem text="Alignment Window" target="alMenu">
- <tocitem text="File Menu" target="alwFile"/>
- <tocitem text="Edit Menu" target="alwEdit"/>
- <tocitem text="Select Menu" target="alwSelect"/>
- <tocitem text="View Menu" target="alwView"/>
- <tocitem text="Format Menu" target="alwFormat"/>
- <tocitem text="Colour Menu" target="alwColour"/>
- <tocitem text="Calculation Menu" target="alwCalc"/>
- <tocitem text="Web Service Menu" target="wsMenu"/>
- <tocitem text="Annotation Menus" target="annotMenus"/>
- <tocitem text="Popup Menu" target="popMenu"/>
- </tocitem>
- </tocitem>
- <tocitem text="Preferences" target="preferences"/>
- <tocitem text="Memory Settings" target="memory" expand="false">
- <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
- </tocitem>
- <tocitem text="Command Line" target="commandline" expand="false">
- <tocitem text="Command Line Arguments" target="clarguments"/>
- </tocitem>
-</tocitem>
-<tocitem text="Useful information" expa nd="true">
- <tocitem text="Amino Acid Table" target="aminoAcids"/>
- <tocitem text="Amino Acid Properties" target="aaProperties"/>
- <tocitem text="The Genetic Code" target="geneticCode"/>
-</tocitem>
-</toc>