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