help/helpTOC.xml

   1 <?xml version="1.0" encoding="ISO-8859-1"  ?>
   2 <!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) *
   3         Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview.
   4         * * Jalview is free software: you can redistribute it and/or * modify it
   5         under the terms of the GNU General Public License * as published by the Free
   6         Software Foundation, either version 3 * of the License, or (at your option)
   7         any later version. * * Jalview is distributed in the hope that it will be
   8         useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of
   9         MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General
  10         Public License for more details. * * You should have received a copy of the
  11         GNU General Public License * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
  12         * The Jalview Authors are detailed in the 'AUTHORS' file. -->
  13 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
  14 <toc version="1.0">
  15         <tocitem text="Jalview Documentation" target="home" expand="true">
  16                 <tocitem text="What's new" target="new" expand="true">
  17                         <tocitem text="Annotation from Structure" target="xsspannotation"
  18                                 expand="false" />
  19                         <tocitem text="Annotation Panel Menu" target="alwAnnotations" />
  20                         <tocitem text="Add reference annotation" target="popMenuAddref" />
  21                         <tocitem text="Colour By Annotation" target="colours.annotation" />
  22                         <tocitem text="Chimera Viewer" target="chimera" />
  23                         <tocitem text="Structure Preferences" target="strucprefs" />
  24                 </tocitem>
  25                 <tocitem text="Editing Alignments" target="edit" />
  26                 <tocitem text="Cursor Mode" target="cursor" />
  27                 <tocitem text="Key Strokes" target="keys" />
  28                 <tocitem text="Input / Output" target="io" />
  29                 <tocitem text="Making Figures" target="export" />
  30                 <tocitem text="Hidden Regions" target="hiddenRegions" />
  31                 <tocitem text="Multiple Views" target="multipleviews" />
  32                 <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
  33                 <tocitem text="Fetching Sequences" target="seqfetch" />
  34                 <tocitem text="Nucleic Acid Support" target="nucleicAcids"
  35                         expand="false">
  36                         <tocitem text="Viewing RNA structure" target="varna" />
  37                         <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
  38                         <tocitem text="RNA Helices coloring" target="colours.rnahelices" />
  39                 </tocitem>
  40                 <tocitem text="Sequence Features" target="seqfeatures" expand="false">
  41                         <tocitem text="Sequence Feature Settings" target="seqfeatures.settings" />
  42                         <tocitem text="Sequence Features File" target="features.fileformat" />
  43                         <tocitem text="Feature Colourschemes" target="features.featureschemes" />
  44                         <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
  45                         <tocitem text="Editing Sequence Features" target="seqfeatedit" />
  46                         <tocitem text="DAS Feature Retrieval" target="das.viewing" />
  47                         <tocitem text="DAS Feature Settings" target="das.settings" />
  48                         <tocitem text="HTML annotation report" target="io.seqreport" />
  49                 </tocitem>
  50                 <tocitem text="Web Services" target="webservice" expand="false">
  51                         <tocitem text="JABAWS" target="jabaws" />
  52                         <tocitem text="Web Service Preferences" target="wsprefs" />
  53                         <tocitem text="Web Service Parameters" target="wsparams" />
  54                         <tocitem text="Sequence Alignment" target="msaservice"
  55                                 expand="false">
  56                                 <tocitem text="Multiple Alignment Subjobs" target="msaservice" />
  57                         </tocitem>
  58                         <tocitem text="Secondary Structure Prediction" target="jnet" />
  59                         <tocitem text="RNAalifold RNA Secondary Structure Prediction"
  60                                 target="rnaalifold" />
  61                         <tocitem text="Protein Disorder Prediction" target="disorder" />
  62                         <tocitem text="Alignment Conservation Analysis" target="aacon" />
  63                         <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws" />
  64                         <tocitem text="Sequence Retrieval" target="seqfetch" />
  65                         <tocitem text="Database Reference Retrieval" target="dbreffetcher" />
  66                         <tocitem text="DAS Feature Retrieval" target="das.viewing" />
  67                 </tocitem>
  68                 <tocitem text="Colour Schemes" target="colours" expand="false">
  69                         <tocitem text="Background Dependent Text Colour" target="backdeptextcol" />
  70                         <tocitem text="ClustalX" target="colours.clustal" />
  71                         <tocitem text="Zappo" target="colours.zappo" />
  72                         <tocitem text="Taylor" target="colours.taylor" />
  73                         <tocitem text="Hydrophobicity" target="colours.hydro" />
  74                         <tocitem text="Helix propensity" target="colours.helix" />
  75                         <tocitem text="Strand propensity" target="colours.strand" />
  76                         <tocitem text="Turn propensity" target="colours.turn" />
  77                         <tocitem text="Buried index" target="colours.buried" />
  78                         <tocitem text="Nucleotide colours" target="colours.nucleotide" />
  79                         <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
  80                         <tocitem text="Blosum62" target="colours.blosum" />
  81                         <tocitem text="by Percentage Identity" target="colours.pid" />
  82                         <tocitem text="User Defined" target="colours.user" />
  83                         <tocitem text="Above Percentage Identity" target="colours.abovepid" />
  84                         <tocitem text="By conservation" target="colours.conservation" />
  85                         <tocitem text="T-COFFEE Scores" target="io.tcoffeescores" />
  86                         <tocitem text="By Annotation" target="colours.annotation" />
  87                         <tocitem text="By RNA Helices" target="colours.rnahelices" />
  88                 </tocitem>
  89                 <tocitem text="Calculations" target="calculations" expand="false">
  90                         <tocitem text="Sorting alignments" target="sorting" />
  91                         <tocitem text="Calculating trees" target="trees" />
  92                         <tocitem text="Principal Component Analysis" target="pca" />
  93                         <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
  94                         <tocitem text="Pairwise Alignments" target="pairwise" />
  95                         <tocitem text="Remove Redundancy" target="redundancy" />
  96                 </tocitem>
  97                 <tocitem text="Sequence Annotations" target="seqannots"
  98                         expand="true">
  99                         <tocitem text="Annotation from Structure" target="xsspannotation"
 100                                 expand="false" />
 101                 </tocitem>
 102                 <tocitem text="Alignment Annotations" target="alannotation"
 103                         expand="false">
 104                         <tocitem text="Conservation" target="calcs.alconserv" />
 105                         <tocitem text="Quality" target="calcs.alquality" />
 106                         <tocitem text="Consensus" target="calcs.consensus" />
 107                         <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
 108                         <tocitem text="Annotations File Format" target="annotations.fileformat" />
 109                 </tocitem>
 110                 <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
 111                         <tocitem text="Jmol Viewer" target="pdbjmol" />
 112                         <tocitem text="Chimera Viewer" target="chimera" />
 113                         <tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
 114                 </tocitem>
 115                 <tocitem text="Viewing RNA structures" target="varna" expand="false">
 116                 </tocitem>
 117                 <tocitem text="VAMSAS Data Exchange" target="vamsas">
 118                         <!-- what can Jalview share with other apps -->
 119                         <!-- what other apps exist -->
 120                 </tocitem>
 121                 <tocitem text="Window Menus" target="menus" expand="false">
 122                         <tocitem text="Desktop Window" target="desktopMenu" />
 123                         <tocitem text="Alignment Window" target="alMenu">
 124                                 <tocitem text="File Menu" target="alwFile" />
 125                                 <tocitem text="Edit Menu" target="alwEdit" />
 126                                 <tocitem text="Select Menu" target="alwSelect" />
 127                                 <tocitem text="View Menu" target="alwView" />
 128                                 <tocitem text="Annotations Menu" target="alwAnnotations" />
 129                                 <tocitem text="Format Menu" target="alwFormat" />
 130                                 <tocitem text="Colour Menu" target="alwColour" />
 131                                 <tocitem text="Calculation Menu" target="alwCalc" />
 132                                 <tocitem text="Web Service Menu" target="wsMenu" />
 133                                 <tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
 134                                 <tocitem text="Popup Menu" target="popMenu" />
 135                         </tocitem>
 136                 </tocitem>
 137                 <tocitem text="Preferences" target="preferences" />
 138                 <tocitem text="Memory Settings" target="memory" expand="false">
 139                         <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp" />
 140                 </tocitem>
 141                 <tocitem text="Command Line" target="commandline" expand="false">
 142                         <tocitem text="Command Line Arguments" target="clarguments" />
 143                         <tocitem text="Groovy Shell" target="groovy" />
 144                 </tocitem>
 145                 <tocitem text="Privacy" target="privacy" />
 146         </tocitem>
 147         <tocitem text="Useful information" expand="true">
 148                 <tocitem text="Amino Acid Table" target="aminoAcids" />
 149                 <tocitem text="Amino Acid Properties" target="aaProperties" />
 150                 <tocitem text="The Genetic Code" target="geneticCode" />
 151                 <tocitem text="Sequence Substitution Matrices" target="subtMatrices" />
 152
 153         </tocitem>
 154 </toc>