<?xml version="1.0" encoding="ISO-8859-1" ?>
+<!--
+ Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
+ Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+
+ This program 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 2
+ of the License, or (at your option) any later version.
+
+ This program 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 this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+-->
<!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="Multiple Views" target="multipleviews"/>
- <tocitem text="Reload and Save" target="reloadsave"/>
- <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
- </tocitem>
- <tocitem text="Release History" target="release"/>
- <tocitem text="Editing Alignments" target ="edit"/>
- <tocitem text="Cursor Mode" target="cursor"/>
+ <tocitem text="Release History" target="release"/>
+ <tocitem text="Sequence Retrieval" target="seqfetch"/>
+ <tocitem text="VAMSAS Interoperation" target="vamsas"/>
+ </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="User Defined Sequence Features" target="search"/>
+ <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 text="Multiple Alignment Subjobs" target="msaservice"/>
</tocitem>
<tocitem text="Secondary Structure Prediction" target="jnet"/>
+ <tocitem text="Sequence Retrieval" target="seqfetch"/>
+ <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="ClustalX" target="colours.clustal"/>
<tocitem text="Zappo" target="colours.zappo"/>
<tocitem text="Taylor" target="colours.taylor"/>
<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 text="File Menu" target="alwFile"/>
- <tocitem text="Edit Menu" target="alwEdit"/>
- <tocitem text="View Menu" target="alwView"/>
+ <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="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 text="Groovy Shell" target="groovy"/>
+ </tocitem>
+ <tocitem text="Privacy" target="privacy"/>
</tocitem>
-<tocitem text="Useful information" expand="true">
+<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"/>
git://source.jalview.org / jalview.git / blobdiff