1 <?xml version="1.0" encoding="ISO-8859-1" ?>
3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
21 <tocitem text="Jalview Documentation" target="home" expand="true" >
22 <tocitem text="What's new" target="new" expand="true">
23 <tocitem text="Graduated Feature Colours" target="features.featureschemes"/>
24 <tocitem text="Sort by Features" target="seqfeatures.settings"/>
25 <tocitem text="Envision2 Service" target="webservice"/>
26 <tocitem text="Release History" target="release"/>
28 <tocitem text="Editing Alignments" target ="edit"/>
29 <tocitem text="Cursor Mode" target="cursor"/>
30 <tocitem text="Key Strokes" target="keys"/>
31 <tocitem text="Input / Output" target="io"/>
32 <tocitem text="Making Figures" target="export"/>
33 <tocitem text="Hidden Regions" target="hiddenRegions"/>
34 <tocitem text="Multiple Views" target="multipleviews"/>
35 <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
36 <tocitem text="Fetching Sequences" target="seqfetch"/>
37 <tocitem text="Sequence Features" target="seqfeatures" expand="false">
38 <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
39 <tocitem text="Sequence Features File" target="features.fileformat"/>
40 <tocitem text="Feature Colourschemes" target="features.featureschemes"/>
41 <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
42 <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
43 <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
44 <tocitem text="DAS Feature Settings" target="das.settings"/>
46 <tocitem text="Web Services" target="webservice" expand="false">
47 <tocitem text="Sequence Alignment" target="msaservice" expand="false">
48 <tocitem text="Clustal Alignment" target="clustal"/>
49 <tocitem text="Muscle Alignment" target="muscle"/>
50 <tocitem text="MAFFT Alignment" target="mafft"/>
51 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
53 <tocitem text="Secondary Structure Prediction" target="jnet"/>
54 <tocitem text="Sequence Retrieval" target="seqfetch"/>
55 <tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
56 <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
58 <tocitem text="Colour Schemes" target="colours" expand="false">
59 <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
60 <tocitem text="ClustalX" target="colours.clustal"/>
61 <tocitem text="Zappo" target="colours.zappo"/>
62 <tocitem text="Taylor" target="colours.taylor"/>
63 <tocitem text="Hydrophobicity" target="colours.hydro"/>
64 <tocitem text="Helix propensity" target="colours.helix"/>
65 <tocitem text="Strand propensity" target="colours.strand"/>
66 <tocitem text="Turn propensity" target="colours.turn"/>
67 <tocitem text="Buried index" target="colours.buried"/>
68 <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
69 <tocitem text="Blosum62" target="colours.blosum"/>
70 <tocitem text="by Percentage Identity" target="colours.pid"/>
71 <tocitem text="User Defined" target="colours.user"/>
72 <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
73 <tocitem text="By conservation" target="colours.conservation"/>
74 <tocitem text="By Annotation" target="colours.annotation"/>
76 <tocitem text="Calculations" target="calculations" expand="false">
77 <tocitem text="Sorting alignments" target="sorting"/>
78 <tocitem text="Calculating trees" target="trees"/>
79 <tocitem text="Principal Component Analysis" target="pca"/>
80 <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
81 <tocitem text="Pairwise Alignments" target="pairwise"/>
82 <tocitem text="Remove Redundancy" target="redundancy"/>
84 <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
85 <tocitem text="Conservation" target="calcs.alconserv"/>
86 <tocitem text="Quality" target="calcs.alquality"/>
87 <tocitem text="Consensus" target="calcs.consensus"/>
88 <tocitem text="Annotations File Format" target="annotations.fileformat"/>
90 <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
91 <tocitem text="Jmol Viewer" target="pdbjmol"/>
92 <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
94 <tocitem text="VAMSAS Data Exchange" target="vamsas">
95 <!-- what can Jalview share with other apps -->
96 <!-- what other apps exist -->
98 <tocitem text="Window Menus" target="menus" expand="false">
99 <tocitem text="Desktop Window" target="desktopMenu"/>
100 <tocitem text="Alignment Window" target="alMenu">
101 <tocitem text="File Menu" target="alwFile"/>
102 <tocitem text="Edit Menu" target="alwEdit"/>
103 <tocitem text="Select Menu" target="alwSelect"/>
104 <tocitem text="View Menu" target="alwView"/>
105 <tocitem text="Format Menu" target="alwFormat"/>
106 <tocitem text="Colour Menu" target="alwColour"/>
107 <tocitem text="Calculation Menu" target="alwCalc"/>
108 <tocitem text="Web Service Menu" target="wsMenu"/>
109 <tocitem text="Annotation Menus" target="annotMenus"/>
110 <tocitem text="Popup Menu" target="popMenu"/>
113 <tocitem text="Preferences" target="preferences"/>
114 <tocitem text="Memory Settings" target="memory" expand="false">
115 <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
117 <tocitem text="Command Line" target="commandline" expand="false">
118 <tocitem text="Command Line Arguments" target="clarguments"/>
119 <tocitem text="Groovy Shell" target="groovy"/>
121 <tocitem text="Privacy" target="privacy"/>
123 <tocitem text="Useful information" expa nd="true">
124 <tocitem text="Amino Acid Table" target="aminoAcids"/>
125 <tocitem text="Amino Acid Properties" target="aaProperties"/>
126 <tocitem text="The Genetic Code" target="geneticCode"/>