help/helpTOC.xml

   1 <?xml version="1.0" encoding="ISO-8859-1"  ?>\r
   2 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">\r
   3 <toc version="1.0">\r
   4 <tocitem text="Jalview Documentation" target="home" expand="true" >\r
   5         <tocitem text="What's new" target="new" expand="false">\r
   6                 <tocitem text="DAS Feature Fetching" target="das.settings"/>\r
   7                 <tocitem text="Hide Regions" target="hiddenRegions"/>\r
   8                 <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>\r
   9                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>\r
  10                 <tocitem text="MAFFT Alignment" target="mafft"/>\r
  11         </tocitem>\r
  12         <tocitem text="Release History" target="release"/>\r
  13         <tocitem text="Editing Alignments" target ="edit"/>     \r
  14         <tocitem text="Cursor Mode" target="cursor"/>\r
  15         <tocitem text="Key Strokes" target="keys"/>\r
  16         <tocitem text="Input / Output" target="io"/>\r
  17         <tocitem text="Making figures" target="export"/>\r
  18         <tocitem text="Hidden Regions" target="hiddenRegions"/>\r
  19         <tocitem text="Viewing PDB Files" target="viewingpdbs"/>\r
  20         <tocitem text="Sequence Features" target="seqfeatures" expand="false">\r
  21           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
  22           <tocitem text="Sequence Features File" target="features.fileformat"/>\r
  23           <tocitem text="User Defined Sequence Features" target="search"/>\r
  24           <tocitem text="DAS Features Settings" target="das.viewing"/>\r
  25         </tocitem>\r
  26         <tocitem text="Web Services" target="webservice" expand="false">\r
  27           <tocitem text="Sequence Alignment" target="msaservice" expand="false">\r
  28                 <tocitem text="Clustal Alignment" target="clustal"/>\r
  29                 <tocitem text="Muscle Alignment" target="muscle"/>\r
  30                 <tocitem text="MAFFT Alignment" target="mafft"/>\r
  31             </tocitem>\r
  32           <tocitem text="Secondary Structure Prediction" target="jnet"/>\r
  33         </tocitem>\r
  34         <tocitem text="Colour Schemes" target="colours" expand="false">\r
  35                 <tocitem text="ClustalX" target="colours.clustal"/>\r
  36                 <tocitem text="Zappo" target="colours.zappo"/>\r
  37                 <tocitem text="Taylor" target="colours.taylor"/>\r
  38                 <tocitem text="Hydrophobicity" target="colours.hydro"/>\r
  39                 <tocitem text="Helix propensity" target="colours.helix"/>\r
  40                 <tocitem text="Strand propensity" target="colours.strand"/>\r
  41                 <tocitem text="Turn propensity" target="colours.turn"/>\r
  42                 <tocitem text="Buried index" target="colours.buried"/>\r
  43                 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>\r
  44                 <tocitem text="Blosum62" target="colours.blosum"/>\r
  45                 <tocitem text="by Percentage Identity" target="colours.pid"/>   \r
  46                 <tocitem text="User Defined" target="colours.user"/>\r
  47                 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>\r
  48                 <tocitem text="By conservation" target="colours.conservation"/>\r
  49                 <tocitem text="By Annotation" target="colours.annotation"/>\r
  50         </tocitem>\r
  51         <tocitem text="Calculations" target="calculations" expand="false">\r
  52                 <tocitem text="Sorting alignments" target="sorting"/>\r
  53                 <tocitem text="Calculating trees" target="trees"/>\r
  54                 <tocitem text="Principal Component Analysis" target="pca"/>\r
  55                 <tocitem text="Pairwise Alignments" target="pairwise"/>\r
  56                 <tocitem text="Remove Redundancy" target="redundancy"/>\r
  57         </tocitem>\r
  58         <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
  59           <tocitem text="Conservation" target="calcs.alconserv"/>\r
  60           <tocitem text="Quality" target="calcs.alquality"/>\r
  61           <tocitem text="Consensus" target="calcs.consensus"/>\r
  62           <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
  63         </tocitem>\r
  64         <tocitem text="Window Menus" target="menus" expand="false">\r
  65                 <tocitem text="Desktop Window" target="desktopMenu"/>\r
  66                 <tocitem text="Alignment Window" target="alMenu">\r
  67                 <tocitem text="File Menu" target="alwFile"/>\r
  68                 <tocitem text="Edit Menu" target="alwEdit"/> \r
  69                 <tocitem text="View Menu" target="alwView"/> \r
  70                 <tocitem text="Colour Menu" target="alwColour"/>\r
  71                 <tocitem text="Calculation Menu" target="alwCalc"/>\r
  72                 <tocitem text="Web Service Menu" target="wsMenu"/>\r
  73                 <tocitem text="Annotation Menus" target="annotMenus"/>\r
  74                 <tocitem text="Popup Menu" target="popMenu"/>\r
  75                 </tocitem>\r
  76         </tocitem>\r
  77         <tocitem text="Memory Settings" target="memory" expand="false">\r
  78           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>\r
  79           </tocitem>\r
  80 </tocitem>\r
  81 <tocitem text="Useful information" expand="true">\r
  82         <tocitem text="Amino Acid Table" target="aminoAcids"/>\r
  83         <tocitem text="Amino Acid Properties" target="aaProperties"/>\r
  84         <tocitem text="The Genetic Code" target="geneticCode"/>\r
  85 </tocitem>\r
  86 </toc>\r