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">
4 <tocitem text="Jalview Documentation" target="home" expand="true" >
5 <tocitem text="What's new" target="new" expand="true">
6 <tocitem text="Multiple Views" target="multipleviews"/>
7 <tocitem text="Reload and Save" target="reloadsave"/>
8 <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
10 <tocitem text="Release History" target="release"/>
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="Viewing PDB Files" target="viewingpdbs"/>
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="search"/>
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"/>
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"/>
33 <tocitem text="Secondary Structure Prediction" target="jnet"/>
35 <tocitem text="Colour Schemes" target="colours" expand="false">
36 <tocitem text="ClustalX" target="colours.clustal"/>
37 <tocitem text="Zappo" target="colours.zappo"/>
38 <tocitem text="Taylor" target="colours.taylor"/>
39 <tocitem text="Hydrophobicity" target="colours.hydro"/>
40 <tocitem text="Helix propensity" target="colours.helix"/>
41 <tocitem text="Strand propensity" target="colours.strand"/>
42 <tocitem text="Turn propensity" target="colours.turn"/>
43 <tocitem text="Buried index" target="colours.buried"/>
44 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
45 <tocitem text="Blosum62" target="colours.blosum"/>
46 <tocitem text="by Percentage Identity" target="colours.pid"/>
47 <tocitem text="User Defined" target="colours.user"/>
48 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
49 <tocitem text="By conservation" target="colours.conservation"/>
50 <tocitem text="By Annotation" target="colours.annotation"/>
52 <tocitem text="Calculations" target="calculations" expand="false">
53 <tocitem text="Sorting alignments" target="sorting"/>
54 <tocitem text="Calculating trees" target="trees"/>
55 <tocitem text="Principal Component Analysis" target="pca"/>
56 <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
57 <tocitem text="Pairwise Alignments" target="pairwise"/>
58 <tocitem text="Remove Redundancy" target="redundancy"/>
60 <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
61 <tocitem text="Conservation" target="calcs.alconserv"/>
62 <tocitem text="Quality" target="calcs.alquality"/>
63 <tocitem text="Consensus" target="calcs.consensus"/>
64 <tocitem text="Annotations File Format" target="annotations.fileformat"/>
66 <tocitem text="Window Menus" target="menus" expand="false">
67 <tocitem text="Desktop Window" target="desktopMenu"/>
68 <tocitem text="Alignment Window" target="alMenu">
69 <tocitem text="File Menu" target="alwFile"/>
70 <tocitem text="Edit Menu" target="alwEdit"/>
71 <tocitem text="View Menu" target="alwView"/>
72 <tocitem text="Colour Menu" target="alwColour"/>
73 <tocitem text="Calculation Menu" target="alwCalc"/>
74 <tocitem text="Web Service Menu" target="wsMenu"/>
75 <tocitem text="Annotation Menus" target="annotMenus"/>
76 <tocitem text="Popup Menu" target="popMenu"/>
79 <tocitem text="Memory Settings" target="memory" expand="false">
80 <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
83 <tocitem text="Useful information" expand="true">
84 <tocitem text="Amino Acid Table" target="aminoAcids"/>
85 <tocitem text="Amino Acid Properties" target="aaProperties"/>
86 <tocitem text="The Genetic Code" target="geneticCode"/>