help/helpTOC.xml

   1 <?xml version="1.0" encoding="ISO-8859-1"  ?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
   4  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18 -->
  19 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
  20 <toc version="1.0">
  21 <tocitem text="Jalview Documentation" target="home" expand="true" >
  22         <tocitem text="What's new" target="new" expand="true">
  23       <tocitem text="Jaba Web Services" target="jabaws"/>
  24       <tocitem text="Enhanced Jmol/Jalview interaction" target="pdbjmol"/>
  25           <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
  26       <tocitem text="Default Colouring preferences" target=""/>
  27         </tocitem>
  28     <tocitem text="Editing Alignments" target ="edit"/>
  29     <tocitem text="Cursor Mode" target="cursor"/>
  30         <tocitem text="Key Strokes" target="keys"/>
  31         <tocitem text="Input / Output" target="io"/>
  32         <tocitem text="Making Figures" target="export"/>
  33         <tocitem text="Hidden Regions" target="hiddenRegions"/>
  34         <tocitem text="Multiple Views" target="multipleviews"/>
  35         <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
  36         <tocitem text="Fetching Sequences" target="seqfetch"/>
  37         <tocitem text="Sequence Features" target="seqfeatures" expand="false">
  38           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
  39           <tocitem text="Sequence Features File" target="features.fileformat"/>
  40           <tocitem text="Feature Colourschemes" target="features.featureschemes"/>
  41           <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
  42                   <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
  43           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
  44           <tocitem text="DAS Feature Settings" target="das.settings"/>
  45         </tocitem>
  46         <tocitem text="Web Services" target="webservice" expand="false">
  47         <tocitem text="JABAWS" target="jabaws"/>
  48         <tocitem text="Web Service Preferences" target="wsprefs"/>
  49         <tocitem text="Web Service Parameters" target="wsparams"/>
  50         <tocitem text="Sequence Alignment" target="msaservice" expand="false">
  51                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
  52             </tocitem>
  53           <tocitem text="Secondary Structure Prediction" target="jnet"/>
  54           <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
  55                 <tocitem text="Sequence Retrieval" target="seqfetch"/>
  56                 <tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
  57                 <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
  58         </tocitem>
  59         <tocitem text="Colour Schemes" target="colours" expand="false">
  60                 <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
  61                 <tocitem text="ClustalX" target="colours.clustal"/>
  62                 <tocitem text="Zappo" target="colours.zappo"/>
  63                 <tocitem text="Taylor" target="colours.taylor"/>
  64                 <tocitem text="Hydrophobicity" target="colours.hydro"/>
  65                 <tocitem text="Helix propensity" target="colours.helix"/>
  66                 <tocitem text="Strand propensity" target="colours.strand"/>
  67                 <tocitem text="Turn propensity" target="colours.turn"/>
  68                 <tocitem text="Buried index" target="colours.buried"/>
  69                 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
  70                 <tocitem text="Blosum62" target="colours.blosum"/>
  71                 <tocitem text="by Percentage Identity" target="colours.pid"/>
  72                 <tocitem text="User Defined" target="colours.user"/>
  73                 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
  74                 <tocitem text="By conservation" target="colours.conservation"/>
  75                 <tocitem text="By Annotation" target="colours.annotation"/>
  76         </tocitem>
  77         <tocitem text="Calculations" target="calculations" expand="false">
  78                 <tocitem text="Sorting alignments" target="sorting"/>
  79                 <tocitem text="Calculating trees" target="trees"/>
  80                 <tocitem text="Principal Component Analysis" target="pca"/>
  81                 <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
  82                 <tocitem text="Pairwise Alignments" target="pairwise"/>
  83                 <tocitem text="Remove Redundancy" target="redundancy"/>
  84         </tocitem>
  85         <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
  86           <tocitem text="Conservation" target="calcs.alconserv"/>
  87           <tocitem text="Quality" target="calcs.alquality"/>
  88           <tocitem text="Consensus" target="calcs.consensus"/>
  89           <tocitem text="Annotations File Format" target="annotations.fileformat"/>
  90         </tocitem>
  91         <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
  92           <tocitem text="Jmol Viewer" target="pdbjmol"/>
  93           <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
  94         </tocitem>
  95         <tocitem text="VAMSAS Data Exchange" target="vamsas">
  96                 <!-- what can Jalview share with other apps -->
  97                 <!-- what other apps exist -->
  98                 </tocitem>
  99         <tocitem text="Window Menus" target="menus" expand="false">
 100                 <tocitem text="Desktop Window" target="desktopMenu"/>
 101                 <tocitem text="Alignment Window" target="alMenu">
 102                 <tocitem text="File Menu" target="alwFile"/>
 103                 <tocitem text="Edit Menu" target="alwEdit"/>
 104                                 <tocitem text="Select Menu" target="alwSelect"/>
 105                 <tocitem text="View Menu" target="alwView"/>
 106                                 <tocitem text="Format Menu" target="alwFormat"/>
 107                 <tocitem text="Colour Menu" target="alwColour"/>
 108                 <tocitem text="Calculation Menu" target="alwCalc"/>
 109                 <tocitem text="Web Service Menu" target="wsMenu"/>
 110                 <tocitem text="Annotation Menus" target="annotMenus"/>
 111                 <tocitem text="Popup Menu" target="popMenu"/>
 112                 </tocitem>
 113         </tocitem>
 114         <tocitem text="Preferences" target="preferences"/>
 115         <tocitem text="Memory Settings" target="memory" expand="false">
 116           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
 117           </tocitem>
 118         <tocitem text="Command Line" target="commandline" expand="false">
 119           <tocitem text="Command Line Arguments" target="clarguments"/>
 120               <tocitem text="Groovy Shell" target="groovy"/>
 121         </tocitem>
 122         <tocitem text="Privacy" target="privacy"/>
 123 </tocitem>
 124 <tocitem text="Useful information" expa nd="true">
 125         <tocitem text="Amino Acid Table" target="aminoAcids"/>
 126         <tocitem text="Amino Acid Properties" target="aaProperties"/>
 127         <tocitem text="The Genetic Code" target="geneticCode"/>
 128 </tocitem>
 129 </toc>