1 <?xml version="1.0" encoding="ISO-8859-1" ?>
2 <!-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) *
3 Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview.
4 * * Jalview is free software: you can redistribute it and/or * modify it
5 under the terms of the GNU General Public License * as published by the Free
6 Software Foundation, either version 3 * of the License, or (at your option)
7 any later version. * * Jalview is distributed in the hope that it will be
8 useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of
9 MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General
10 Public License for more details. * * You should have received a copy of the
11 GNU General Public License * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
12 * The Jalview Authors are detailed in the 'AUTHORS' file. -->
13 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
15 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
16 <tocitem text="Jalview Documentation" target="home" expand="true">
17 <tocitem text="What's new" target="new" expand="true">
18 <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
19 <tocitem text="Annotation Panel Menu" target="alwAnnotations" />
20 <tocitem text="Add reference annotation" target="popMenuAddref" />
21 <tocitem text="Colour By Annotation" target="colours.annotation" />
22 <tocitem text="Chimera Viewer" target="chimera" />
23 <tocitem text="Structure Preferences" target="strucprefs" />
25 <tocitem text="Editing Alignments" target="edit" />
26 <tocitem text="Cursor Mode" target="cursor" />
27 <tocitem text="Key Strokes" target="keys" />
28 <tocitem text="Input / Output" target="io" />
29 <tocitem text="Making Figures" target="export" />
30 <tocitem text="Hidden Regions" target="hiddenRegions" />
31 <tocitem text="Multiple Views" target="multipleviews" />
32 <tocitem text="Split Frame View" target="splitframe" />
33 <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
34 <tocitem text="Fetching Sequences" target="seqfetch" />
35 <tocitem text="BioJSON v1.0" target="biojson" />
36 <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
37 <tocitem text="PDB Structure Chooser" target="pdbchooser" />
38 <tocitem text="Select columns by annotation" target="selectcolbyannot" />
39 <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
40 <tocitem text="Viewing RNA structure" target="varna" />
41 <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
42 <tocitem text="RNA Helices coloring" target="colours.rnahelices" />
44 <tocitem text="Sequence Features" target="seqfeatures" expand="false">
45 <tocitem text="Sequence Feature Settings" target="seqfeatures.settings" />
46 <tocitem text="Sequence Features File" target="features.fileformat" />
47 <tocitem text="Feature Colourschemes" target="features.featureschemes" />
48 <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
49 <tocitem text="Editing Sequence Features" target="seqfeatedit" />
50 <tocitem text="DAS Feature Retrieval" target="das.viewing" />
51 <tocitem text="DAS Feature Settings" target="das.settings" />
52 <tocitem text="HTML annotation report" target="io.seqreport" />
54 <tocitem text="Web Services" target="webservice" expand="false">
55 <tocitem text="JABAWS" target="jabaws" />
56 <tocitem text="Web Service Preferences" target="wsprefs" />
57 <tocitem text="Web Service Parameters" target="wsparams" />
58 <tocitem text="Sequence Alignment" target="msaservice" expand="false">
59 <tocitem text="Multiple Alignment Subjobs" target="msaservice" />
61 <tocitem text="Secondary Structure Prediction" target="jnet" />
62 <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
63 <tocitem text="Protein Disorder Prediction" target="disorder" />
64 <tocitem text="Alignment Conservation Analysis" target="aacon" />
65 <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws" />
66 <tocitem text="Sequence Retrieval" target="seqfetch" />
67 <tocitem text="Database Reference Retrieval" target="dbreffetcher" />
68 <tocitem text="DAS Feature Retrieval" target="das.viewing" />
70 <tocitem text="Colour Schemes" target="colours" expand="false">
71 <tocitem text="Background Dependent Text Colour" target="backdeptextcol" />
72 <tocitem text="ClustalX" target="colours.clustal" />
73 <tocitem text="Zappo" target="colours.zappo" />
74 <tocitem text="Taylor" target="colours.taylor" />
75 <tocitem text="Hydrophobicity" target="colours.hydro" />
76 <tocitem text="Helix propensity" target="colours.helix" />
77 <tocitem text="Strand propensity" target="colours.strand" />
78 <tocitem text="Turn propensity" target="colours.turn" />
79 <tocitem text="Buried index" target="colours.buried" />
80 <tocitem text="Nucleotide colours" target="colours.nucleotide" />
81 <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
82 <tocitem text="Blosum62" target="colours.blosum" />
83 <tocitem text="by Percentage Identity" target="colours.pid" />
84 <tocitem text="User Defined" target="colours.user" />
85 <tocitem text="Above Percentage Identity" target="colours.abovepid" />
86 <tocitem text="By conservation" target="colours.conservation" />
87 <tocitem text="T-COFFEE Scores" target="io.tcoffeescores" />
88 <tocitem text="By Annotation" target="colours.annotation" />
89 <tocitem text="By RNA Helices" target="colours.rnahelices" />
91 <tocitem text="Calculations" target="calculations" expand="false">
92 <tocitem text="Sorting alignments" target="sorting" />
93 <tocitem text="Calculating trees" target="trees" />
94 <tocitem text="Principal Component Analysis" target="pca" />
95 <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
96 <tocitem text="Pairwise Alignments" target="pairwise" />
97 <tocitem text="Remove Redundancy" target="redundancy" />
98 <tocitem text="Select Column by Annotation" target="calcs.annotation" />
100 <tocitem text="Sequence Annotations" target="seqannots" expand="true">
101 <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
103 <tocitem text="Alignment Annotations" target="alannotation" expand="false">
104 <tocitem text="Conservation" target="calcs.alconserv" />
105 <tocitem text="Quality" target="calcs.alquality" />
106 <tocitem text="Consensus" target="calcs.consensus" />
107 <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
108 <tocitem text="Annotations File Format" target="annotations.fileformat" />
110 <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
111 <tocitem text="Jmol Viewer" target="pdbjmol" />
112 <tocitem text="Chimera Viewer" target="chimera" />
113 <tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
115 <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
116 <tocitem text="VAMSAS Data Exchange" target="vamsas">
117 <!-- what can Jalview share with other apps -->
118 <!-- what other apps exist -->
120 <tocitem text="Window Menus" target="menus" expand="false">
121 <tocitem text="Desktop Window" target="desktopMenu" />
122 <tocitem text="Alignment Window" target="alMenu">
123 <tocitem text="File Menu" target="alwFile" />
124 <tocitem text="Edit Menu" target="alwEdit" />
125 <tocitem text="Select Menu" target="alwSelect" />
126 <tocitem text="View Menu" target="alwView" />
127 <tocitem text="Annotations Menu" target="alwAnnotations" />
128 <tocitem text="Format Menu" target="alwFormat" />
129 <tocitem text="Colour Menu" target="alwColour" />
130 <tocitem text="Calculation Menu" target="alwCalc" />
131 <tocitem text="Web Service Menu" target="wsMenu" />
132 <tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
133 <tocitem text="Popup Menu" target="popMenu" />
136 <tocitem text="Preferences" target="preferences" />
137 <tocitem text="Memory Settings" target="memory" expand="false"/>
138 <tocitem text="Command Line" target="commandline" expand="false">
139 <tocitem text="Command Line Arguments" target="clarguments" />
140 <tocitem text="Groovy Shell" target="groovy" />
142 <tocitem text="Privacy" target="privacy" />
144 <tocitem text="Useful information" expand="true">
145 <tocitem text="Amino Acid Table" target="aminoAcids" />
146 <tocitem text="Amino Acid Properties" target="aaProperties" />
147 <tocitem text="The Genetic Code" target="geneticCode" />
148 <tocitem text="Sequence Substitution Matrices" target="subtMatrices" />