<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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/>.
+ * 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">
<toc version="1.0">
<tocitem text="Jalview Documentation" target="home" expand="true" >
- <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="Viewing RNA structure" target="varna" />
- <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
- <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
- <tocitem text="HTML annotation report" target="io.seqreport"/>
- <tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
- <tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
- <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
- <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
- <tocitem text="DNA or Protein PCA calculation" target="pca"/>
- <tocitem text="Normalised sequence logo display" target="calcs.consensus"/>
- </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="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
+ <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
+ <tocitem text="View all representative PDB structures" target="viewingpdbs.reps"/>
+ <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
+ </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 Alignment Subjobs" target="msaservice"/>
</tocitem>
<tocitem text="Secondary Structure Prediction" target="jnet"/>
+ <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="Pairwise Alignments" target="pairwise"/>
<tocitem text="Remove Redundancy" target="redundancy"/>
</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>
<tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
<tocitem text="Jmol Viewer" target="pdbjmol"/>
+ <tocitem text="Chimera Viewer" target="chimera"/>
<tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
</tocitem>
<tocitem text="Viewing RNA structures" target="varna" expand="false"> </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 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="Annotations Menu" target="alwAnnotations"/>
+ <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 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">