1 <?xml version="1.0" encoding="ISO-8859-1" ?>
3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
24 <tocitem text="Jalview Documentation" target="home" expand="true">
25 <tocitem text="What's new" target="new" expand="true">
26 <tocitem text="Latest Release Notes" target="release"/>
27 <tocitem text="Structure Chooser" target="pdbchooser"/>
28 <tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
31 <tocitem text="Editing Alignments" target="edit" />
32 <tocitem text="Cursor Mode" target="cursor" />
33 <tocitem text="Key Strokes" target="keys" />
35 <tocitem text="Input / Output" target="io" expand="false">
36 <tocitem text="BioJSON v1.0" target="biojson" />
39 <tocitem text="Making Figures" target="export" expand="false">
40 <tocitem text="BioJS MSA Viewer" target="biojsmsa" />
43 <tocitem text="Hidden Regions" target="hiddenRegions" />
44 <tocitem text="Multiple Views" target="multipleviews" />
45 <tocitem text="Split Frame View" target="splitframe" />
46 <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
47 <tocitem text="Fetching Sequences" target="seqfetch" />
49 <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
51 <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
52 <tocitem text="Viewing RNA structure" target="varna" />
53 <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
54 <tocitem text="RNA Helices coloring" target="colours.rnahelices" />
57 <tocitem text="Sequence Features" target="seqfeatures" expand="false">
58 <tocitem text="Sequence Feature Settings" target="seqfeatures.settings" />
59 <tocitem text="Sequence Features File" target="features.fileformat" />
60 <tocitem text="Feature Colourschemes" target="features.featureschemes" />
61 <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
62 <tocitem text="Editing Sequence Features" target="seqfeatedit" />
63 <tocitem text="HTML annotation report" target="io.seqreport" />
66 <tocitem text="Web Services" target="webservice" expand="false">
67 <tocitem text="JABAWS" target="jabaws" />
68 <tocitem text="Web Service Preferences" target="wsprefs" />
69 <tocitem text="Web Service Parameters" target="wsparams" />
70 <tocitem text="Sequence Alignment" target="msaservice" expand="false">
71 <tocitem text="Multiple Alignment Subjobs" target="msaservice" />
73 <tocitem text="Secondary Structure Prediction" target="jpred" />
74 <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
75 <tocitem text="Protein Disorder Prediction" target="disorder" />
76 <tocitem text="Alignment Conservation Analysis" target="aacon" />
77 <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws" />
78 <tocitem text="Sequence Retrieval" target="seqfetch" />
79 <tocitem text="Database Reference Retrieval" target="dbreffetcher" />
82 <tocitem text="Colour Schemes" target="colours" expand="false">
83 <tocitem text="Background Dependent Text Colour" target="backdeptextcol" />
84 <tocitem text="ClustalX" target="colours.clustal" />
85 <tocitem text="Zappo" target="colours.zappo" />
86 <tocitem text="Taylor" target="colours.taylor" />
87 <tocitem text="Hydrophobicity" target="colours.hydro" />
88 <tocitem text="Helix propensity" target="colours.helix" />
89 <tocitem text="Strand propensity" target="colours.strand" />
90 <tocitem text="Turn propensity" target="colours.turn" />
91 <tocitem text="Buried index" target="colours.buried" />
92 <tocitem text="Nucleotide colours" target="colours.nucleotide" />
93 <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
94 <tocitem text="Blosum62" target="colours.blosum" />
95 <tocitem text="by Percentage Identity" target="colours.pid" />
96 <tocitem text="User Defined" target="colours.user" />
97 <tocitem text="Above Percentage Identity" target="colours.abovepid" />
98 <tocitem text="By conservation" target="colours.conservation" />
99 <tocitem text="T-COFFEE Scores" target="io.tcoffeescores" />
100 <tocitem text="By Annotation" target="colours.annotation" />
101 <tocitem text="By RNA Helices" target="colours.rnahelices" />
104 <tocitem text="Calculations" expand="false">
105 <tocitem text="Sorting alignments" target="sorting" />
106 <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
107 <tocitem text="Calculating trees" target="trees" />
108 <tocitem text="Principal Component Analysis" target="pca" />
110 <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
111 <tocitem text="Pairwise Alignments" target="pairwise" />
112 <tocitem text="Remove Redundancy" target="redundancy" />
113 <tocitem text="Reference Sequences" target="referenceseq" />
116 <tocitem text="Sequence Annotations" target="seqannots" expand="true">
117 <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
120 <tocitem text="Alignment Annotations" target="alannotation" expand="false">
121 <tocitem text="Conservation" target="calcs.alconserv" />
122 <tocitem text="Quality" target="calcs.alquality" />
123 <tocitem text="Consensus" target="calcs.consensus" />
124 <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
125 <tocitem text="Annotations File Format" target="annotations.fileformat" />
126 <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
128 <tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
129 <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
130 <tocitem text="PDB Structure Chooser" target="pdbchooser" />
131 <tocitem text="Jmol Viewer" target="pdbjmol" />
132 <tocitem text="Chimera Viewer" target="chimera" />
134 <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
135 <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
136 <tocitem text="Configuring URL Links" target="linksprefs" />
138 <tocitem text="VAMSAS Data Exchange" target="vamsas">
139 <!-- what can Jalview share with other apps -->
140 <!-- what other apps exist -->
142 <tocitem text="Window Menus" target="menus" expand="false">
143 <tocitem text="Desktop Window" target="desktopMenu" />
144 <tocitem text="Alignment Window" target="alMenu">
145 <tocitem text="File Menu" target="alwFile" />
146 <tocitem text="Edit Menu" target="alwEdit" />
147 <tocitem text="Select Menu" target="alwSelect" />
148 <tocitem text="View Menu" target="alwView" />
149 <tocitem text="Annotations Menu" target="alwAnnotations" />
150 <tocitem text="Format Menu" target="alwFormat" />
151 <tocitem text="Colour Menu" target="alwColour" />
152 <tocitem text="Calculate Menu" target="alwCalc" />
153 <tocitem text="Web Service Menu" target="wsMenu" />
154 <tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
155 <tocitem text="Popup Menu" target="popMenu" />
158 <tocitem text="Preferences" target="preferences" />
159 <tocitem text="Memory Settings" target="memory" expand="false"/>
160 <tocitem text="Scripting with Groovy" target="groovy">
161 <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
163 <tocitem text="Command Line" target="commandline" expand="false">
164 <tocitem text="Command Line Arguments" target="clarguments" />
166 <tocitem text="Privacy" target="privacy" />
168 <tocitem text="Useful information" expand="true">
169 <tocitem text="Amino Acid Table" target="aminoAcids" />
170 <tocitem text="Amino Acid Properties" target="aaProperties" />
171 <tocitem text="The Genetic Code" target="geneticCode" />
172 <tocitem text="Sequence Substitution Matrices" target="subtMatrices" />