-<?xml version="1.0" encoding="ISO-8859-1" ?>\r
-<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">\r
-<toc version="1.0">\r
-<tocitem text="Jalview Documentation" target="home" expand="true" >\r
- <tocitem text="What's new" target="new" expand="false">\r
- <tocitem text="Cursor Mode" target="cursor"/>\r
- <tocitem text="Selection Area Based Editing"\r
- target="edit.selareas"/>\r
- <tocitem text="User Defined Sequence Features" target="search"/>\r
- <tocitem text="Sequence Feature Groups" target="seqfeatures"/>\r
- <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
- <tocitem text="Extended Sequence Feature Input File" target="features.fileformat"/>\r
- <tocitem text="Annotations File" target="annotations.fileformat"/>\r
- </tocitem>\r
- <tocitem text="Release History" target="release"/>\r
- <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
- <tocitem text="Conservation" target="calcs.alconserv"/>\r
- <tocitem text="Quality" target="calcs.alquality"/>\r
- <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
- </tocitem>\r
- <tocitem text="Input / Output" target="io"/>\r
- <tocitem text="Key Strokes" target="keys"/>\r
- <tocitem text="Making figures" target="export"/>\r
- <tocitem text="Editing Alignments" target ="edit"/>\r
- <tocitem text="Sequence Features" target="seqfeatures" expand="false">\r
- <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
- <tocitem text="Sequence Features File" target="features.fileformat"/>\r
- </tocitem>\r
- <tocitem text="Web Services" target="webservice" expand="false">\r
- <tocitem text="Clustal Alignment" target="clustal"/>\r
- <tocitem text="Muscle Alignment" target="muscle"/>\r
- <tocitem text="JNet Prediction" target="jnet"/>\r
- </tocitem>\r
- <tocitem text="Colour Schemes" target="colours" expand="false">\r
- <tocitem text="ClustalX" target="colours.clustal"/>\r
- <tocitem text="Zappo" target="colours.zappo"/>\r
- <tocitem text="Taylor" target="colours.taylor"/>\r
- <tocitem text="Hydrophobicity" target="colours.hydro"/>\r
- <tocitem text="Helix propensity" target="colours.helix"/>\r
- <tocitem text="Strand propensity" target="colours.strand"/>\r
- <tocitem text="Turn propensity" target="colours.turn"/>\r
- <tocitem text="Buried index" target="colours.buried"/>\r
- <tocitem text="Nucleotide colours" target="colours.nucleotide"/>\r
- <tocitem text="Blosum62" target="colours.blosum"/>\r
- <tocitem text="by Percentage Identity" target="colours.pid"/> \r
- <tocitem text="User Defined" target="colours.user"/>\r
- <tocitem text="Above Percentage Identity" target="colours.abovepid"/>\r
- <tocitem text="By conservation" target="colours.conservation"/>\r
- <tocitem text="By Annotation" target="colours.annotation"/>\r
- </tocitem>\r
- <tocitem text="Calculations" target="calculations" expand="false">\r
- <tocitem text="Sorting alignments" target="sorting"/>\r
- <tocitem text="Calculating trees" target="trees"/>\r
- <tocitem text="Principal Component Analysis" target="pca"/>\r
- <tocitem text="Pairwise Alignments" target="pairwise"/>\r
- <tocitem text="Remove Redundancy" target="redundancy"/>\r
- </tocitem>\r
- <tocitem text="Window Menus" target="menus" expand="false">\r
- <tocitem text="Desktop Window" target="desktopMenu"/>\r
- <tocitem text="Alignment Window" target="alMenu">\r
- <tocitem text="File Menu" target="alwFile"/>\r
- <tocitem text="Edit Menu" target="alwEdit"/> \r
- <tocitem text="View Menu" target="alwView"/> \r
- <tocitem text="Colour Menu" target="alwColour"/>\r
- <tocitem text="Calculation Menu" target="alwCalc"/>\r
- <tocitem text="Web Service Menu" target="wsMenu"/>\r
- <tocitem text="Annotation Menus" target="annotMenus"/>\r
- <tocitem text="Popup Menu" target="popMenu"/>\r
- </tocitem>\r
- </tocitem>\r
- <tocitem text="Memory Settings" target="memory" expand="false">\r
- <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>\r
- </tocitem>\r
-</tocitem>\r
-<tocitem text="Useful information" expand="true">\r
- <tocitem text="Amino Acid Table" target="aminoAcids"/>\r
- <tocitem text="Amino Acid Properties" target="aaProperties"/>\r
- <tocitem text="The Genetic Code" target="geneticCode"/>\r
-</tocitem>\r
-</toc>\r
+<?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, J Engelhardt, LM Lui, 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="Viewing RNA structure" target="varna" />
+ <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
+ <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
+ </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="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="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="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>
+ <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="Hydrophobicity" target="colours.hydro"/>
+ <tocitem text="Helix propensity" target="colours.helix"/>
+ <tocitem text="Strand propensity" target="colours.strand"/>
+ <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="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="Calculating trees" target="trees"/>
+ <tocitem text="Principal Component Analysis" target="pca"/>
+ <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
+ <tocitem text="Pairwise Alignments" target="pairwise"/>
+ <tocitem text="Remove Redundancy" target="redundancy"/>
+ </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>
+ <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="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>
+ <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" expa nd="true">
+ <tocitem text="Amino Acid Table" target="aminoAcids"/>
+ <tocitem text="Amino Acid Properties" target="aaProperties"/>
+ <tocitem text="The Genetic Code" target="geneticCode"/>
+</tocitem>
+</toc>
git://source.jalview.org / jalview.git / blobdiff