help/helpTOC.xml

   1 <?xml version="1.0" encoding="ISO-8859-1"  ?>
   2 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
   3 <toc version="1.0">
   4 <tocitem text="Jalview Documentation" target="home" expand="true" >
   5         <tocitem text="What's new" target="new" expand="true">
   6       <tocitem text="Release History" target="release"/>
   7           <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
   8           <tocitem text="Mapping between Sequences" target="seqmappings"/>
   9                 <tocitem text="VAMSAS Interoperation" target="vamsas"/>
  10     </tocitem>
  11     <tocitem text="Editing Alignments" target ="edit"/>
  12     <tocitem text="Cursor Mode" target="cursor"/>
  13         <tocitem text="Key Strokes" target="keys"/>
  14         <tocitem text="Input / Output" target="io"/>
  15         <tocitem text="Making Figures" target="export"/>
  16         <tocitem text="Hidden Regions" target="hiddenRegions"/>
  17         <tocitem text="Multiple Views" target="multipleviews"/>
  18         <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
  19         <tocitem text="Fetching Sequences" target="seqfetch"/>
  20         <tocitem text="Sequence Features" target="seqfeatures" expand="false">
  21           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
  22           <tocitem text="Sequence Features File" target="features.fileformat"/>
  23           <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
  24                   <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
  25           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
  26           <tocitem text="DAS Feature Settings" target="das.settings"/>
  27         </tocitem>
  28         <tocitem text="Web Services" target="webservice" expand="false">
  29           <tocitem text="Sequence Alignment" target="msaservice" expand="false">
  30                 <tocitem text="Clustal Alignment" target="clustal"/>
  31                 <tocitem text="Muscle Alignment" target="muscle"/>
  32                 <tocitem text="MAFFT Alignment" target="mafft"/>
  33                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
  34             </tocitem>
  35           <tocitem text="Secondary Structure Prediction" target="jnet"/>
  36                 <tocitem text="Sequence Retrieval" target="seqfetch"/>
  37                 <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
  38         </tocitem>
  39         <tocitem text="Colour Schemes" target="colours" expand="false">
  40                 <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
  41                 <tocitem text="ClustalX" target="colours.clustal"/>
  42                 <tocitem text="Zappo" target="colours.zappo"/>
  43                 <tocitem text="Taylor" target="colours.taylor"/>
  44                 <tocitem text="Hydrophobicity" target="colours.hydro"/>
  45                 <tocitem text="Helix propensity" target="colours.helix"/>
  46                 <tocitem text="Strand propensity" target="colours.strand"/>
  47                 <tocitem text="Turn propensity" target="colours.turn"/>
  48                 <tocitem text="Buried index" target="colours.buried"/>
  49                 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
  50                 <tocitem text="Blosum62" target="colours.blosum"/>
  51                 <tocitem text="by Percentage Identity" target="colours.pid"/>
  52                 <tocitem text="User Defined" target="colours.user"/>
  53                 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
  54                 <tocitem text="By conservation" target="colours.conservation"/>
  55                 <tocitem text="By Annotation" target="colours.annotation"/>
  56         </tocitem>
  57         <tocitem text="Calculations" target="calculations" expand="false">
  58                 <tocitem text="Sorting alignments" target="sorting"/>
  59                 <tocitem text="Calculating trees" target="trees"/>
  60                 <tocitem text="Principal Component Analysis" target="pca"/>
  61                 <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
  62                 <tocitem text="Pairwise Alignments" target="pairwise"/>
  63                 <tocitem text="Remove Redundancy" target="redundancy"/>
  64         </tocitem>
  65         <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
  66           <tocitem text="Conservation" target="calcs.alconserv"/>
  67           <tocitem text="Quality" target="calcs.alquality"/>
  68           <tocitem text="Consensus" target="calcs.consensus"/>
  69           <tocitem text="Annotations File Format" target="annotations.fileformat"/>
  70         </tocitem>
  71         <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
  72           <tocitem text="Jmol Viewer" target="pdbjmol"/>
  73           <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
  74         </tocitem>
  75         <tocitem text="VAMSAS Data Exchange" target="vamsas">
  76                 <!-- what can Jalview share with other apps -->
  77                 <!-- what other apps exist -->
  78                 </tocitem>
  79         <tocitem text="Window Menus" target="menus" expand="false">
  80                 <tocitem text="Desktop Window" target="desktopMenu"/>
  81                 <tocitem text="Alignment Window" target="alMenu">
  82                 <tocitem text="File Menu" target="alwFile"/>
  83                 <tocitem text="Edit Menu" target="alwEdit"/>
  84                                 <tocitem text="Select Menu" target="alwSelect"/>
  85                 <tocitem text="View Menu" target="alwView"/>
  86                                 <tocitem text="Format Menu" target="alwFormat"/>
  87                 <tocitem text="Colour Menu" target="alwColour"/>
  88                 <tocitem text="Calculation Menu" target="alwCalc"/>
  89                 <tocitem text="Web Service Menu" target="wsMenu"/>
  90                 <tocitem text="Annotation Menus" target="annotMenus"/>
  91                 <tocitem text="Popup Menu" target="popMenu"/>
  92                 </tocitem>
  93         </tocitem>
  94         <tocitem text="Preferences" target="preferences"/>
  95         <tocitem text="Memory Settings" target="memory" expand="false">
  96           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
  97           </tocitem>
  98         <tocitem text="Command Line" target="commandline" expand="false">
  99           <tocitem text="Command Line Arguments" target="clarguments"/>
 100               <tocitem text="Groovy Shell" target="groovy"/>
 101         </tocitem>
 102 </tocitem>
 103 <tocitem text="Useful information" expa nd="true">
 104         <tocitem text="Amino Acid Table" target="aminoAcids"/>
 105         <tocitem text="Amino Acid Properties" target="aaProperties"/>
 106         <tocitem text="The Genetic Code" target="geneticCode"/>
 107 </tocitem>
 108 </toc>