<?xml version="1.0" encoding="ISO-8859-1" ?>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
<!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="Enhanced Jmol/Jalview interaction" target="pdbjmol"/>
+ <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
+ <tocitem text="Jalview News Reader" target="newsreader"/>
+ <tocitem text="Sort alignments associated with tree" target="treeviewer"/>
+ <tocitem text="Default Annotation preferences" target="colours.annotation"/>
+ <tocitem text="Jaba Web Services" target="jabaws"/>
+ </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="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="Viewing Trees" target="treeviewer" expand="false"/>
+ <tocitem text="Fetching Sequences" target="seqfetch"/>
<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="Feature Colourschemes" target="features.featureschemes"/>
<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="JABAWS" target="jabaws"/>
+ <tocitem text="Web Service Preferences" target="wsprefs"/>
+ <tocitem text="Web Service Parameters" target="wsparams"/>
+ <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="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
+ <tocitem text="Sequence Retrieval" target="seqfetch"/>
+ <tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
+ <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
</tocitem>
<tocitem text="Colour Schemes" target="colours" expand="false">
<tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
<tocitem text="Pairwise Alignments" target="pairwise"/>
<tocitem text="Remove Redundancy" target="redundancy"/>
</tocitem>
- <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
+ <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="Viewing PDB Files" target="viewingpdbs" expand="false">
+ <tocitem text="Jmol Viewer" target="pdbjmol"/>
+ <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
+ </tocitem>
+ <tocitem text="VAMSAS Data Exchange" target="vamsas">
+ <!-- what can Jalview share with other apps -->
+ <!-- what other apps exist -->
+ </tocitem>
<tocitem text="Window Menus" target="menus" expand="false">
<tocitem text="Desktop Window" target="desktopMenu"/>
<tocitem text="Alignment Window" target="alMenu">
</tocitem>
<tocitem text="Command Line" target="commandline" expand="false">
<tocitem text="Command Line Arguments" target="clarguments"/>
+ <tocitem text="Groovy Shell" target="groovy"/>
</tocitem>
+ <tocitem text="Privacy" target="privacy"/>
</tocitem>
<tocitem text="Useful information" expa nd="true">
<tocitem text="Amino Acid Table" target="aminoAcids"/>
git://source.jalview.org / jalview.git / blobdiff