help/helpTOC.xml

   1 <?xml version="1.0" encoding="ISO-8859-1"  ?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   4  * Copyright (C) 2014 The Jalview Authors
   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
  11  * of the License, or (at your option) any later version.
  12  *
  13  * Jalview is distributed in the hope that it will be useful, but
  14  * WITHOUT ANY WARRANTY; without even the implied warranty
  15  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  16  * PURPOSE.  See the GNU General Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License
  19  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  20  * The Jalview Authors are detailed in the 'AUTHORS' file.
  21 -->
  22 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
  23 <toc version="1.0">
  24 <tocitem text="Jalview Documentation" target="home" expand="true" >
  25  <tocitem text="What's new" target="new" expand="true">
  26     <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
  27     <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
  28     <tocitem text="View all representative PDB structures" target="viewingpdbs.reps"/>
  29     <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
  30   </tocitem>
  31   <tocitem text="Editing Alignments" target ="edit"/>
  32   <tocitem text="Cursor Mode" target="cursor"/>
  33   <tocitem text="Key Strokes" target="keys"/>
  34         <tocitem text="Input / Output" target="io"/>
  35         <tocitem text="Making Figures" target="export"/>
  36         <tocitem text="Hidden Regions" target="hiddenRegions"/>
  37         <tocitem text="Multiple Views" target="multipleviews"/>
  38         <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
  39         <tocitem text="Fetching Sequences" target="seqfetch"/>
  40         <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
  41                 <tocitem text="Viewing RNA structure" target="varna" />
  42                 <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
  43                 <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
  44         </tocitem>
  45         <tocitem text="Sequence Features" target="seqfeatures" expand="false">
  46           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
  47           <tocitem text="Sequence Features File" target="features.fileformat"/>
  48           <tocitem text="Feature Colourschemes" target="features.featureschemes"/>
  49           <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
  50                   <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
  51           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
  52           <tocitem text="DAS Feature Settings" target="das.settings"/>
  53           <tocitem text="HTML annotation report" target="io.seqreport"/>
  54         </tocitem>
  55         <tocitem text="Web Services" target="webservice" expand="false">
  56         <tocitem text="JABAWS" target="jabaws"/>
  57         <tocitem text="Web Service Preferences" target="wsprefs"/>
  58         <tocitem text="Web Service Parameters" target="wsparams"/>
  59         <tocitem text="Sequence Alignment" target="msaservice" expand="false">
  60                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
  61             </tocitem>
  62           <tocitem text="Secondary Structure Prediction" target="jnet"/>
  63           <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
  64           <tocitem text="Protein Disorder Prediction" target="disorder"/>
  65           <tocitem text="Alignment Conservation Analysis" target="aacon"/>
  66           <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
  67                 <tocitem text="Sequence Retrieval" target="seqfetch"/>
  68                 <tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
  69                 <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
  70         </tocitem>
  71         <tocitem text="Colour Schemes" target="colours" expand="false">
  72                 <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
  73                 <tocitem text="ClustalX" target="colours.clustal"/>
  74                 <tocitem text="Zappo" target="colours.zappo"/>
  75                 <tocitem text="Taylor" target="colours.taylor"/>
  76                 <tocitem text="Hydrophobicity" target="colours.hydro"/>
  77                 <tocitem text="Helix propensity" target="colours.helix"/>
  78                 <tocitem text="Strand propensity" target="colours.strand"/>
  79                 <tocitem text="Turn propensity" target="colours.turn"/>
  80                 <tocitem text="Buried index" target="colours.buried"/>
  81                 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
  82                 <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine"/>
  83                 <tocitem text="Blosum62" target="colours.blosum"/>
  84                 <tocitem text="by Percentage Identity" target="colours.pid"/>
  85                 <tocitem text="User Defined" target="colours.user"/>
  86                 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
  87                 <tocitem text="By conservation" target="colours.conservation"/>
  88     <tocitem text="T-COFFEE Scores" target="io.tcoffeescores"/>
  89                 <tocitem text="By Annotation" target="colours.annotation"/>
  90                 <tocitem text="By RNA Helices" target="colours.rnahelices"/>
  91         </tocitem>
  92         <tocitem text="Calculations" target="calculations" expand="false">
  93                 <tocitem text="Sorting alignments" target="sorting"/>
  94                 <tocitem text="Calculating trees" target="trees"/>
  95                 <tocitem text="Principal Component Analysis" target="pca"/>
  96                 <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
  97                 <tocitem text="Pairwise Alignments" target="pairwise"/>
  98                 <tocitem text="Remove Redundancy" target="redundancy"/>
  99         </tocitem>
 100         <tocitem text="Sequence Annotations" target="seqannots" expand="true">
 101                 <tocitem text="Annotation from Structure" target="xsspannotation" expand="false"/>
 102         </tocitem>
 103         <tocitem text="Alignment Annotations" target ="alannotation" 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">   </tocitem>
 116         <tocitem text="VAMSAS Data Exchange" target="vamsas">
 117                 <!-- what can Jalview share with other apps -->
 118                 <!-- what other apps exist -->
 119                 </tocitem>
 120         <tocitem text="Window Menus" target="menus" expand="false">
 121                 <tocitem text="Desktop Window" target="desktopMenu"/>
 122                 <tocitem text="Alignment Window" target="alMenu">
 123             <tocitem text="File Menu" target="alwFile"/>
 124             <tocitem text="Edit Menu" target="alwEdit"/>
 125                         <tocitem text="Select Menu" target="alwSelect"/>
 126             <tocitem text="View Menu" target="alwView"/>
 127             <tocitem text="Annotations Menu" target="alwAnnotations"/>
 128                         <tocitem text="Format Menu" target="alwFormat"/>
 129             <tocitem text="Colour Menu" target="alwColour"/>
 130             <tocitem text="Calculation Menu" target="alwCalc"/>
 131                         <tocitem text="Web Service Menu" target="wsMenu"/>
 132                         <tocitem text="Annotation Panel Menu" target="annotPanelMenu"/>
 133                         <tocitem text="Popup Menu" target="popMenu"/>
 134         </tocitem>
 135         </tocitem>
 136         <tocitem text="Preferences" target="preferences"/>
 137         <tocitem text="Memory Settings" target="memory" expand="false">
 138           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
 139           </tocitem>
 140         <tocitem text="Command Line" target="commandline" expand="false">
 141           <tocitem text="Command Line Arguments" target="clarguments"/>
 142               <tocitem text="Groovy Shell" target="groovy"/>
 143         </tocitem>
 144         <tocitem text="Privacy" target="privacy"/>
 145 </tocitem>
 146 <tocitem text="Useful information" expand="true">
 147         <tocitem text="Amino Acid Table" target="aminoAcids"/>
 148         <tocitem text="Amino Acid Properties" target="aaProperties"/>
 149         <tocitem text="The Genetic Code" target="geneticCode"/>
 150         <tocitem text="Sequence Substitution Matrices" target="subtMatrices"/>
 151
 152 </tocitem>
 153 </toc>