5e69a230c5c86fd93b5b14d51de8709674be17d9
[jalview.git] / 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="EBI Sequence Fetcher" target="seqfetch"/>\r
7                 <tocitem text="New Output Format Controls" target="preferences"/>\r
8                 <tocitem text="Enhanced PDB Viewer" target="viewingpdbs"/>\r
9                 <tocitem text="Sequence Feature Styles" target="seqfeatures"/>\r
10         </tocitem>\r
11         <tocitem text="Release History" target="release"/>\r
12         <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
13           <tocitem text="Conservation" target="calcs.alconserv"/>\r
14           <tocitem text="Quality" target="calcs.alquality"/>\r
15         </tocitem>\r
16         <tocitem text="Input / Output" target="io"/>\r
17         <tocitem text="Key Strokes" target="keys"/>\r
18         <tocitem text="Making figures" target="export"/>\r
19         <tocitem text="Editing Alignments" target ="edit"/>\r
20         <tocitem text="Web Services" target="webservice" expand="false">\r
21                 <tocitem text="Clustal Alignment" target="clustal"/>\r
22                 <tocitem text="Muscle Alignment" target="muscle"/>\r
23                 <tocitem text="JNet Prediction" target="jnet"/>\r
24         </tocitem>\r
25         <tocitem text="Colour Schemes" target="colours" expand="false">\r
26                 <tocitem text="ClustalX" target="colours.clustal"/>\r
27                 <tocitem text="Zappo" target="colours.zappo"/>\r
28                 <tocitem text="Taylor" target="colours.taylor"/>\r
29                 <tocitem text="Hydrophobicity" target="colours.hydro"/>\r
30                 <tocitem text="Helix propensity" target="colours.helix"/>\r
31                 <tocitem text="Strand propensity" target="colours.strand"/>\r
32                 <tocitem text="Turn propensity" target="colours.turn"/>\r
33                 <tocitem text="Buried index" target="colours.buried"/>\r
34                 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>\r
35                 <tocitem text="Blosum62" target="colours.blosum"/>\r
36                 <tocitem text="by Percentage Identity" target="colours.pid"/>   \r
37                 <tocitem text="User Defined" target="colours.user"/>\r
38                 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>\r
39                 <tocitem text="By conservation" target="colours.conservation"/>\r
40         </tocitem>\r
41         <tocitem text="Calculations" target="calculations" expand="false">\r
42                 <tocitem text="Sorting alignments" target="sorting"/>\r
43                 <tocitem text="Calculating trees" target="trees"/>\r
44                 <tocitem text="Principal Component Analysis" target="pca"/>\r
45                 <tocitem text="Pairwise Alignments" target="pairwise"/>\r
46                 <tocitem text="Remove Redundancy" target="redundancy"/>\r
47         </tocitem>\r
48         <tocitem text="Window Menus" target="menus" expand="false">\r
49                 <tocitem text="Desktop Window" target="desktopMenu"/>\r
50                 <tocitem text="Alignment Window" target="alMenu">\r
51                 <tocitem text="File Menu" target="alwFile"/>\r
52                 <tocitem text="Edit Menu" target="alwEdit"/> \r
53                 <tocitem text="View Menu" target="alwView"/> \r
54                 <tocitem text="Colour Menu" target="alwColour"/>\r
55                 <tocitem text="Calculation Menu" target="alwCalc"/>\r
56                                 <tocitem text="Web Service Menu" target="wsMenu"/>\r
57                 <tocitem text="Annotation Menus" target="annotMenus"/>\r
58                 <tocitem text="Popup Menu" target="popMenu"/>\r
59                 </tocitem>\r
60         </tocitem>\r
61         <tocitem text="Memory Settings" target="memory" expand="false">\r
62           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>\r
63           </tocitem>\r
64 </tocitem>\r
65 <tocitem text="Useful information" expand="true">\r
66         <tocitem text="Amino Acid Table" target="aminoAcids"/>\r
67         <tocitem text="Amino Acid Properties" target="aaProperties"/>\r
68         <tocitem text="The Genetic Code" target="geneticCode"/>\r
69 </tocitem>\r
70 </toc>\r