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="Coding Region Sequence Features" target="cdnafeatures"/>
  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="Sequence Features" target="seqfeatures" expand="false">
  19           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
  20           <tocitem text="Sequence Features File" target="features.fileformat"/>
  21           <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
  22                   <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
  23           <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
  24           <tocitem text="DAS Feature Settings" target="das.settings"/>
  25         </tocitem>
  26         <tocitem text="Web Services" target="webservice" expand="false">
  27           <tocitem text="Sequence Alignment" target="msaservice" expand="false">
  28                 <tocitem text="Clustal Alignment" target="clustal"/>
  29                 <tocitem text="Muscle Alignment" target="muscle"/>
  30                 <tocitem text="MAFFT Alignment" target="mafft"/>
  31                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
  32             </tocitem>
  33           <tocitem text="Secondary Structure Prediction" target="jnet"/>
  34         </tocitem>
  35         <tocitem text="Colour Schemes" target="colours" expand="false">
  36                 <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
  37                 <tocitem text="ClustalX" target="colours.clustal"/>
  38                 <tocitem text="Zappo" target="colours.zappo"/>
  39                 <tocitem text="Taylor" target="colours.taylor"/>
  40                 <tocitem text="Hydrophobicity" target="colours.hydro"/>
  41                 <tocitem text="Helix propensity" target="colours.helix"/>
  42                 <tocitem text="Strand propensity" target="colours.strand"/>
  43                 <tocitem text="Turn propensity" target="colours.turn"/>
  44                 <tocitem text="Buried index" target="colours.buried"/>
  45                 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
  46                 <tocitem text="Blosum62" target="colours.blosum"/>
  47                 <tocitem text="by Percentage Identity" target="colours.pid"/>
  48                 <tocitem text="User Defined" target="colours.user"/>
  49                 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
  50                 <tocitem text="By conservation" target="colours.conservation"/>
  51                 <tocitem text="By Annotation" target="colours.annotation"/>
  52         </tocitem>
  53         <tocitem text="Calculations" target="calculations" expand="false">
  54                 <tocitem text="Sorting alignments" target="sorting"/>
  55                 <tocitem text="Calculating trees" target="trees"/>
  56                 <tocitem text="Principal Component Analysis" target="pca"/>
  57                 <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
  58                 <tocitem text="Pairwise Alignments" target="pairwise"/>
  59                 <tocitem text="Remove Redundancy" target="redundancy"/>
  60         </tocitem>
  61         <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
  62           <tocitem text="Conservation" target="calcs.alconserv"/>
  63           <tocitem text="Quality" target="calcs.alquality"/>
  64           <tocitem text="Consensus" target="calcs.consensus"/>
  65           <tocitem text="Annotations File Format" target="annotations.fileformat"/>
  66         </tocitem>
  67         <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
  68           <tocitem text="Jmol Viewer" target="pdbjmol"/>
  69           <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
  70         </tocitem>
  71         <tocitem text="Window Menus" target="menus" expand="false">
  72                 <tocitem text="Desktop Window" target="desktopMenu"/>
  73                 <tocitem text="Alignment Window" target="alMenu">
  74                 <tocitem text="File Menu" target="alwFile"/>
  75                 <tocitem text="Edit Menu" target="alwEdit"/>
  76                                 <tocitem text="Select Menu" target="alwSelect"/>
  77                 <tocitem text="View Menu" target="alwView"/>
  78                                 <tocitem text="Format Menu" target="alwFormat"/>
  79                 <tocitem text="Colour Menu" target="alwColour"/>
  80                 <tocitem text="Calculation Menu" target="alwCalc"/>
  81                 <tocitem text="Web Service Menu" target="wsMenu"/>
  82                 <tocitem text="Annotation Menus" target="annotMenus"/>
  83                 <tocitem text="Popup Menu" target="popMenu"/>
  84                 </tocitem>
  85         </tocitem>
  86         <tocitem text="Preferences" target="preferences"/>
  87         <tocitem text="Memory Settings" target="memory" expand="false">
  88           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
  89           </tocitem>
  90         <tocitem text="Command Line" target="commandline" expand="false">
  91           <tocitem text="Command Line Arguments" target="clarguments"/>
  92         </tocitem>
  93 </tocitem>
  94 <tocitem text="Useful information" expa nd="true">
  95         <tocitem text="Amino Acid Table" target="aminoAcids"/>
  96         <tocitem text="Amino Acid Properties" target="aaProperties"/>
  97         <tocitem text="The Genetic Code" target="geneticCode"/>
  98 </tocitem>
  99 </toc>