help/helpTOC.xml

   1 <?xml version="1.0" encoding="ISO-8859-1"  ?>
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   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ 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 <toc version="1.0">
  23 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
  24         <tocitem text="Jalview Documentation" target="home" expand="true">
  25                         <tocitem text="What's new" target="new" expand="true">
  26                                 <tocitem text="Latest Release Notes" target="release"/>
  27         <tocitem text="Calculations Dialog" target="calcs.dialog"/>
  28                                 <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
  29                                 <tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
  30                                 <tocitem text="Omit hidden regions in Overview" target="overview"/>
  31                                 <tocitem text="Show gaps as grey in overview" target="overviewprefs"/>
  32                                 <tocitem text="identifers.org for URL Links" target="linksprefs" />
  33                                 <tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
  34                 </tocitem>
  35
  36                 <tocitem text="Editing Alignments" target="edit" />
  37                 <tocitem text="Cursor Mode" target="cursor" />
  38                 <tocitem text="Key Strokes" target="keys" />
  39
  40                 <tocitem text="Input / Output" target="io" expand="false">
  41                         <tocitem text="BioJSON v1.0" target="biojson" />
  42                 </tocitem>
  43
  44                 <tocitem text="Making Figures" target="export" expand="false">
  45                         <tocitem text="BioJS MSA Viewer" target="biojsmsa" />
  46                 </tocitem>
  47
  48                 <tocitem text="Hidden Regions" target="hiddenRegions" />
  49                 <tocitem text="Multiple Views" target="multipleviews" />
  50                 <tocitem text="Split Frame View" target="splitframe" />
  51                 <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
  52                 <tocitem text="Fetching Sequences" target="seqfetch" />
  53
  54                 <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
  55
  56                 <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
  57                         <tocitem text="Viewing RNA structure" target="varna" />
  58                         <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
  59                         <tocitem text="RNA Helices coloring" target="colours.rnahelices" />
  60                 </tocitem>
  61
  62                 <tocitem text="Sequence Features" target="seqfeatures" expand="false">
  63                         <tocitem text="Sequence Feature Settings" target="seqfeatures.settings" />
  64                         <tocitem text="Sequence Features File" target="features.fileformat" />
  65                         <tocitem text="Feature Colourschemes" target="features.featureschemes" />
  66                         <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
  67                         <tocitem text="Editing Sequence Features" target="seqfeatedit" />
  68                         <tocitem text="DAS Feature Retrieval" target="das.viewing" />
  69                         <tocitem text="DAS Feature Settings" target="das.settings" />
  70                         <tocitem text="HTML annotation report" target="io.seqreport" />
  71                 </tocitem>
  72
  73                 <tocitem text="Web Services" target="webservice" expand="false">
  74                         <tocitem text="JABAWS" target="jabaws" />
  75                         <tocitem text="Web Service Preferences" target="wsprefs" />
  76                         <tocitem text="Web Service Parameters" target="wsparams" />
  77                         <tocitem text="Sequence Alignment" target="msaservice"  expand="false">
  78                                 <tocitem text="Multiple Alignment Subjobs" target="msaservice" />
  79                         </tocitem>
  80                         <tocitem text="Secondary Structure Prediction" target="jpred" />
  81                         <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
  82                         <tocitem text="Protein Disorder Prediction" target="disorder" />
  83                         <tocitem text="Alignment Conservation Analysis" target="aacon" />
  84                         <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws" />
  85                         <tocitem text="Sequence Retrieval" target="seqfetch" />
  86                         <tocitem text="Database Reference Retrieval" target="dbreffetcher" />
  87                         <tocitem text="DAS Feature Retrieval" target="das.viewing" />
  88                 </tocitem>
  89
  90                 <tocitem text="Colour Schemes" target="colours" expand="false">
  91                         <tocitem text="Background Dependent Text Colour" target="backdeptextcol" />
  92                         <tocitem text="ClustalX" target="colours.clustal" />
  93                         <tocitem text="Zappo" target="colours.zappo" />
  94                         <tocitem text="Taylor" target="colours.taylor" />
  95                         <tocitem text="Hydrophobicity" target="colours.hydro" />
  96                         <tocitem text="Helix propensity" target="colours.helix" />
  97                         <tocitem text="Strand propensity" target="colours.strand" />
  98                         <tocitem text="Turn propensity" target="colours.turn" />
  99                         <tocitem text="Buried index" target="colours.buried" />
 100                         <tocitem text="Nucleotide colours" target="colours.nucleotide" />
 101                         <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
 102                         <tocitem text="Blosum62" target="colours.blosum" />
 103                         <tocitem text="by Percentage Identity" target="colours.pid" />
 104                         <tocitem text="User Defined" target="colours.user" />
 105                         <tocitem text="Above Percentage Identity" target="colours.abovepid" />
 106                         <tocitem text="By conservation" target="colours.conservation" />
 107                         <tocitem text="T-COFFEE Scores" target="io.tcoffeescores" />
 108                         <tocitem text="By Annotation" target="colours.annotation" />
 109                         <tocitem text="By RNA Helices" target="colours.rnahelices" />
 110                 </tocitem>
 111
 112                 <tocitem text="Calculations" expand="false">
 113                         <tocitem text="Sorting alignments" target="sorting" />
 114                         <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
 115                           <tocitem text="Calculating trees" target="trees" />
 116                           <tocitem text="Principal Component Analysis" target="pca" />
 117                         </tocitem>
 118                         <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
 119                         <tocitem text="Pairwise Alignments" target="pairwise" />
 120                         <tocitem text="Remove Redundancy" target="redundancy" />
 121                         <tocitem text="Reference Sequences" target="referenceseq" />
 122                 </tocitem>
 123
 124                 <tocitem text="Sequence Annotations" target="seqannots" expand="true">
 125                         <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
 126                 </tocitem>
 127
 128                 <tocitem text="Alignment Annotations" target="alannotation" expand="false">
 129                         <tocitem text="Conservation" target="calcs.alconserv" />
 130                         <tocitem text="Quality" target="calcs.alquality" />
 131                         <tocitem text="Consensus" target="calcs.consensus" />
 132                         <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
 133                         <tocitem text="Annotations File Format" target="annotations.fileformat" />
 134                         <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
 135                 </tocitem>
 136                 <tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
 137                         <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
 138                         <tocitem text="PDB Structure Chooser" target="pdbchooser" />
 139                         <tocitem text="Jmol Viewer" target="pdbjmol" />
 140                         <tocitem text="Chimera Viewer" target="chimera" />
 141                 </tocitem>
 142                 <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
 143                 <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
 144                     <tocitem text="Configuring URL Links" target="linksprefs" />
 145                 </tocitem>
 146                 <tocitem text="VAMSAS Data Exchange" target="vamsas">
 147                         <!-- what can Jalview share with other apps -->
 148                         <!-- what other apps exist -->
 149                 </tocitem>
 150                 <tocitem text="Window Menus" target="menus" expand="false">
 151                         <tocitem text="Desktop Window" target="desktopMenu" />
 152                         <tocitem text="Alignment Window" target="alMenu">
 153                                 <tocitem text="File Menu" target="alwFile" />
 154                                 <tocitem text="Edit Menu" target="alwEdit" />
 155                                 <tocitem text="Select Menu" target="alwSelect" />
 156                                 <tocitem text="View Menu" target="alwView" />
 157                                 <tocitem text="Annotations Menu" target="alwAnnotations" />
 158                                 <tocitem text="Format Menu" target="alwFormat" />
 159                                 <tocitem text="Colour Menu" target="alwColour" />
 160                                 <tocitem text="Calculate Menu" target="alwCalc" />
 161                                 <tocitem text="Web Service Menu" target="wsMenu" />
 162                                 <tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
 163                                 <tocitem text="Popup Menu" target="popMenu" />
 164                         </tocitem>
 165                 </tocitem>
 166                 <tocitem text="Preferences" target="preferences" />
 167                 <tocitem text="Memory Settings" target="memory" expand="false"/>
 168                 <tocitem text="Scripting with Groovy" target="groovy">
 169                         <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
 170                 </tocitem>
 171                 <tocitem text="Command Line" target="commandline" expand="false">
 172                         <tocitem text="Command Line Arguments" target="clarguments" />
 173                 </tocitem>
 174                 <tocitem text="Privacy" target="privacy" />
 175         </tocitem>
 176         <tocitem text="Useful information" expand="true">
 177                 <tocitem text="Amino Acid Table" target="aminoAcids" />
 178                 <tocitem text="Amino Acid Properties" target="aaProperties" />
 179                 <tocitem text="The Genetic Code" target="geneticCode" />
 180                 <tocitem text="Sequence Substitution Matrices" target="subtMatrices" />
 181
 182         </tocitem>
 183 </toc>