-<?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="EBI Sequence Fetcher" target="seqfetch"/>\r
- <tocitem text="New Output Format Controls" target="preferences"/>\r
- <tocitem text="Enhanced PDB Viewer" target="pdbviewer"/>\r
- <tocitem text="Sequence Feature Styles" target="seqfeatures"/>\r
- </tocitem>\r
- <tocitem text="Release History" target="release"/>\r
- <tocitem text="Alignment Annotations" target ="alannotation"/>\r
- \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="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>\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"/>\r
-</tocitem>\r
-<tocitem text="Useful information" expand="true">\r
- <tocitem text="Amino Acid Table" target="aminoAcids"/>\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 ($$Version-Rel$$)
+ * 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="Retrieval from ENSEMBL" target="ensemblfetch" />
+ <tocitem text="UniProt Free Text Search" target="uniprotfetcher" />
+ <tocitem text="SIFTS for mapping PDB structures to UniProt" target="siftsmapping" />
+ <tocitem text="Latest Release Notes" target="release"/>
+ </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" 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="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="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="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="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="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>
+
+ <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="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" 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 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="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>
+ <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
+ <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="Annotations Menu" target="alwAnnotations" />
+ <tocitem text="Format Menu" target="alwFormat" />
+ <tocitem text="Colour Menu" target="alwColour" />
+ <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="Scripting with Groovy" target="groovy">
+ <tocitem text="Groovy Feature Counter example" target="groovy.featurecounter"/>
+ </tocitem>
+ <tocitem text="Command Line" target="commandline" expand="false">
+ <tocitem text="Command Line Arguments" target="clarguments" />
+ </tocitem>
+ <tocitem text="Privacy" target="privacy" />
+ </tocitem>
+ <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