<?xml version="1.0" encoding="ISO-8859-1" ?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) *
- 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">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ -->
<toc version="1.0">
<!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
<tocitem text="Jalview Documentation" target="home" expand="true">
- <tocitem text="What's new" target="new" expand="true">
- <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
- <tocitem text="Annotation Panel Menu" target="alwAnnotations" />
- <tocitem text="Add reference annotation" target="popMenuAddref" />
- <tocitem text="Colour By Annotation" target="colours.annotation" />
- <tocitem text="Chimera Viewer" target="chimera" />
- <tocitem text="Structure Preferences" target="strucprefs" />
+ <tocitem text="What's new" target="new" expand="true">
+ <tocitem text="Latest Release Notes" target="release"/>
+ <tocitem text="Calculations Dialog" target="calcs.dialog"/>
+ <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+ <tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
+ <tocitem text="Omit hidden regions in Overview" target="overview"/>
+ <tocitem text="Show gaps as grey in overview" target="overviewprefs"/>
+ <tocitem text="identifers.org for URL Links" target="linksprefs" />
+ <tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
</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="Input / Output" target="io" expand="false">
+ <tocitem text="BioJSON v1.0" target="biojson" />
+ </tocitem>
+
+ <tocitem text="Making Figures" target="export" expand="false">
+ <tocitem text="BioJS MSA Viewer" target="biojsmsa" />
+ </tocitem>
+
<tocitem text="Hidden Regions" target="hiddenRegions" />
<tocitem text="Multiple Views" target="multipleviews" />
+ <tocitem text="Split Frame View" target="splitframe" />
<tocitem text="Viewing Trees" target="treeviewer" expand="false" />
- <tocitem text="Fetching Sequences" target="seqfetch" />
+ <tocitem text="Fetching Sequences" target="seqfetch" />
+
+ <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
+
<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="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="Web Service Preferences" target="wsprefs" />
<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="Secondary Structure Prediction" target="jpred" />
<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="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="ClustalX" target="colours.clustal" />
<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="Calculations" expand="false">
<tocitem text="Sorting alignments" target="sorting" />
- <tocitem text="Calculating trees" target="trees" />
- <tocitem text="Principal Component Analysis" target="pca" />
+ <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+ <tocitem text="Calculating trees" target="trees" />
+ <tocitem text="Principal Component Analysis" target="pca" />
+ </tocitem>
<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
<tocitem text="Pairwise Alignments" target="pairwise" />
<tocitem text="Remove Redundancy" target="redundancy" />
+ <tocitem text="Reference Sequences" target="referenceseq" />
</tocitem>
+
<tocitem text="Sequence Annotations" target="seqannots" expand="true">
<tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
</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="RNA Structure Consensus" target="calcs.alstrconsensus" />
<tocitem text="Annotations File Format" target="annotations.fileformat" />
+ <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
</tocitem>
- <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
+ <tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
+ <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
+ <tocitem text="PDB Structure Chooser" target="pdbchooser" />
<tocitem text="Jmol Viewer" target="pdbjmol" />
- <tocitem text="Chimera Viewer" target="chimera" />
- <tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
+ <tocitem text="Chimera Viewer" target="chimera" />
</tocitem>
<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
+ <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
+ <tocitem text="Configuring URL Links" target="linksprefs" />
+ </tocitem>
<tocitem text="VAMSAS Data Exchange" target="vamsas">
<!-- what can Jalview share with other apps -->
<!-- what other apps exist -->
<tocitem text="Annotations Menu" target="alwAnnotations" />
<tocitem text="Format Menu" target="alwFormat" />
<tocitem text="Colour Menu" target="alwColour" />
- <tocitem text="Calculation Menu" target="alwCalc" />
+ <tocitem text="Calculate Menu" target="alwCalc" />
<tocitem text="Web Service Menu" target="wsMenu" />
<tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
<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 text="Memory Settings" target="memory" expand="false"/>
+ <tocitem text="Scripting with Groovy" target="groovy">
+ <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
</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>
git://source.jalview.org / jalview.git / blobdiff