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[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="Search" target="search"/>\r
7                 <tocitem text="Wrap Alignment" target="wrap"/>\r
8                 <tocitem text="Overview Window" target ="overview"/>\r
9                 <tocitem text="Sequence Features" target ="seqfeatures"/>\r
10                 <tocitem text="Alignment Annotations" target ="alannotation"/>\r
11         </tocitem>\r
12         <tocitem text="Input / Output" target="io"/>\r
13         <tocitem text="Making figures" target="export"/>\r
14         <tocitem text="Editing Alignments" target ="edit"/>\r
15         <tocitem text="Web Services" target="webservice" expand="false">\r
16                 <tocitem text="Clustal Alignment" target="clustal"/>\r
17                 <tocitem text="Muscle Alignment" target="muscle"/>\r
18                 <tocitem text="JNet Prediction" target="jnet"/>\r
19         </tocitem>\r
20         <tocitem text="Colour Schemes" target="colours" expand="false">\r
21                 <tocitem text="ClustalX" target="colours.clustal"/>\r
22                 <tocitem text="Zappo" target="colours.zappo"/>\r
23                 <tocitem text="Taylor" target="colours.taylor"/>\r
24                 <tocitem text="Hydrophobicity" target="colours.hydro"/>\r
25                 <tocitem text="Helix propensity" target="colours.helix"/>\r
26                 <tocitem text="Strand propensity" target="colours.strand"/>\r
27                 <tocitem text="Turn propensity" target="colours.turn"/>\r
28                 <tocitem text="Buried index" target="colours.buried"/>\r
29                 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>\r
30                 <tocitem text="Blosum62" target="colours.blosum"/>\r
31                 <tocitem text="by Percentage Identity" target="colours.pid"/>   \r
32                 <tocitem text="User Defined" target="colours.user"/>\r
33                 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>\r
34                 <tocitem text="By conservation" target="colours.conservation"/>\r
35         </tocitem>\r
36         <tocitem text="Calculations" target="calculations" expand="false">\r
37                 <tocitem text="Sorting alignments" target="sorting"/>\r
38                 <tocitem text="Calculating trees" target="trees"/>\r
39                 <tocitem text="Principal Component Analysis" target="pca"/>\r
40                 <tocitem text="Pairwise Alignments" target="pairwise"/>\r
41                 <tocitem text="Remove Redundancy" target="redundancy"/>\r
42         </tocitem>\r
43         <tocitem text="Window Menus" target="menus" expand="false">\r
44                 <tocitem text="Desktop Window" target="desktopMenu"/>\r
45                 <tocitem text="Alignment Window" target="alMenu">\r
46                 <tocitem text="File Menu" target="alwFile"/>\r
47                 <tocitem text="Edit Menu" target="alwEdit"/>  \r
48                 <tocitem text="Colour Menu" target="alwColour"/>\r
49                 <tocitem text="Calculation Menu" target="alwCalc"/>\r
50                                 <tocitem text="Web Service Menu" target="wsMenu"/>\r
51                 <tocitem text="Annotation Menus" target="annotMenus"/>\r
52                 <tocitem text="Popup Menu" target="popMenu"/>\r
53                 </tocitem>\r
54 \r
55         </tocitem>\r
56 </tocitem>\r
57 <tocitem text="Useful information" expand="false">\r
58         <tocitem text="Amino Acid Table" target="aminoAcids"/>\r
59         <tocitem text="The Genetic Code" target="geneticCode"/>\r
60 </tocitem>\r
61 </toc>\r