<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<!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="Jaba Web Services" target="jabaws"/>
- <tocitem text="Enhanced Jmol/Jalview interaction" target="pdbjmol"/>
- <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
- <tocitem text="Default Colouring preferences" target=""/>
- </tocitem>
- <tocitem text="Editing Alignments" target ="edit"/>
- <tocitem text="Cursor Mode" target="cursor"/>
- <tocitem text="Key Strokes" target="keys"/>
+ <tocitem text="What's new" target="new" expand="true">
+ <tocitem text="Protein Disorder Prediction" target="disorder"/>
+ <tocitem text="Alignment Conservation Analysis" target="aacon"/>
+ <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+ <tocitem text="Select columns containing sequence features" target="seqfeatures.settings"/>
+ </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="Multiple Views" target="multipleviews"/>
<tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
<tocitem text="Fetching Sequences" target="seqfetch"/>
+ <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+ <tocitem text="Viewing RNA structure" target="varna" />
+ <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
+ <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
+ </tocitem>
<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="Editing Sequence Features" target="seqfeatedit"/>
<tocitem text="DAS Feature Retrieval" target="das.viewing"/>
<tocitem text="DAS Feature Settings" target="das.settings"/>
+ <tocitem text="HTML annotation report" target="io.seqreport"/>
</tocitem>
<tocitem text="Web Services" target="webservice" expand="false">
<tocitem text="JABAWS" target="jabaws"/>
<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="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+ <tocitem text="Protein Disorder Prediction" target="disorder"/>
+ <tocitem text="Alignment Conservation Analysis" target="aacon"/>
+ <tocitem text="Multi-Harmony Alignment 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 text="Turn propensity" target="colours.turn"/>
<tocitem text="Buried index" target="colours.buried"/>
<tocitem text="Nucleotide colours" target="colours.nucleotide"/>
+ <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine"/>
<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="T-COFFEE Scores" target="io.tcoffeescores"/>
<tocitem text="By Annotation" target="colours.annotation"/>
+ <tocitem text="By RNA Helices" target="colours.rnahelices"/>
</tocitem>
<tocitem text="Calculations" target="calculations" expand="false">
<tocitem text="Sorting alignments" target="sorting"/>
<tocitem text="Remove Redundancy" target="redundancy"/>
</tocitem>
<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
- <tocitem text="Conservation" target="calcs.alconserv"/>
+ <tocitem text="Conservation" target="calcs.alconserv"/>
<tocitem text="Quality" target="calcs.alquality"/>
<tocitem text="Consensus" target="calcs.consensus"/>
+ <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
<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="Viewing RNA structures" target="varna" expand="false"> </tocitem>
<tocitem text="VAMSAS Data Exchange" target="vamsas">
<!-- what can Jalview share with other apps -->
<!-- what other apps exist -->
</tocitem>
<tocitem text="Privacy" target="privacy"/>
</tocitem>
-<tocitem text="Useful information" expa nd="true">
+<tocitem text="Useful information" expand="true">
<tocitem text="Amino Acid Table" target="aminoAcids"/>
<tocitem text="Amino Acid Properties" target="aaProperties"/>
<tocitem text="The Genetic Code" target="geneticCode"/>
+ <tocitem text="Sequence Substitution Matrices" target="subtMatrices"/>
+
</tocitem>
</toc>
git://source.jalview.org / jalview.git / blobdiff