JAL-4059 updated swingjs, Jmol-SwingJS.zip. Insignificantly altered build.gradle.
[jalview.git] / help / help / helpTOC.xml
1 <?xml version="1.0" encoding="ISO-8859-1"  ?>
2 <!--
3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
5  * 
6  * This file is part of Jalview.
7  * 
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.
12  *  
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.
17  * 
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.
21  -->
22 <toc version="1.0">
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="Next Generation Command Line Interface" target="clarguments" />
28                         <tocitem text="AlphaFold PAE Matrices" target="workingwithpae" />
29                         <tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />                            
30                 </tocitem>
31                 
32                 <tocitem text="Editing Alignments" target="edit" />
33                 <tocitem text="Cursor Mode" target="cursor" />
34                 <tocitem text="Key Strokes" target="keys" />
35                 
36                 <tocitem text="Input / Output" target="io" expand="false">
37                         <tocitem text="BioJSON v1.0" target="biojson" />
38                 </tocitem>
39                 
40                 <tocitem text="Making Figures" target="export" expand="false">
41                         <tocitem text="BioJS MSA Viewer" target="biojsmsa" />
42                 </tocitem>
43                 
44                 <tocitem text="Hidden Regions" target="hiddenRegions" />
45                 <tocitem text="Multiple Views" target="multipleviews" />
46                 <tocitem text="Split Frame View" target="splitframe" />
47                 <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
48                 <tocitem text="Fetching Sequences" target="seqfetch" />         
49                 
50                 <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
51                 
52                 <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
53                   <tocitem text="Annotating from VCF" target="importvcf" /> 
54                         <tocitem text="Viewing RNA structure" target="varna" />
55                         <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
56                         <tocitem text="RNA Helices coloring" target="colours.rnahelices" />
57                 </tocitem>
58                 
59                 <tocitem text="Sequence Features" target="seqfeatures" expand="false">
60                         <tocitem text="Sequence Feature Settings" target="seqfeatures.settings" />
61                         <tocitem text="Sequence Features File" target="features.fileformat" />
62                         <tocitem text="Feature Colourschemes" target="features.featureschemes" />
63                         <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
64                         <tocitem text="Editing Sequence Features" target="seqfeatedit" />
65                         <tocitem text="HTML Feature Attributes report" target="seqfeatures.report" />
66                         <tocitem text="HTML annotation report" target="io.seqreport" />
67                 </tocitem>
68                 
69                 <tocitem text="Web Services" target="webservice" expand="false">
70                         <tocitem text="JABAWS" target="jabaws" />
71                         <tocitem text="Web Service Preferences" target="wsprefs" />
72                         <tocitem text="Web Service Parameters" target="wsparams" />
73                         <tocitem text="Sequence Alignment" target="msaservice"  expand="false">
74                                 <tocitem text="Multiple Alignment Subjobs" target="msaservice" />
75                         </tocitem>
76                         <tocitem text="Secondary Structure Prediction" target="jpred" />
77                         <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
78                         <tocitem text="Protein Disorder Prediction" target="disorder" />
79                         <tocitem text="Alignment Conservation Analysis" target="aacon" />
80                         <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws" />
81                         <tocitem text="Sequence Retrieval" target="seqfetch" />
82                         <tocitem text="Database Reference Retrieval" target="dbreffetcher" />                   
83                 </tocitem>
84                 
85                 <tocitem text="Colour Schemes" target="colours" expand="false">
86                         <tocitem text="Background Dependent Text Colour" target="backdeptextcol" />
87                         <tocitem text="ClustalX" target="colours.clustal" />
88                         <tocitem text="Zappo" target="colours.zappo" />
89                         <tocitem text="Taylor" target="colours.taylor" />
90                         <tocitem text="gecos Flower" target="colours.gecos-flower" />
91                         <tocitem text="gecos Blossom" target="colours.gecos-blossom" />
92                         <tocitem text="gecos Sunset" target="colours.gecos-sunset" />
93                         <tocitem text="gecos Ocean" target="colours.gecos-ocean" />
94                         <tocitem text="Hydrophobicity" target="colours.hydro" />
95                         <tocitem text="Helix propensity" target="colours.helix" />
96                         <tocitem text="Strand propensity" target="colours.strand" />
97                         <tocitem text="Turn propensity" target="colours.turn" />
98                         <tocitem text="Buried index" target="colours.buried" />
99                         <tocitem text="Nucleotide colours" target="colours.nucleotide" />
100                         <tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />
101                         <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
102                         <tocitem text="Blosum62" target="colours.blosum" />
103                         <tocitem text="by Percentage Identity" target="colours.pid" />
104                         <tocitem text="User Defined" target="colours.user" />
105                         <tocitem text="Above Percentage Identity" target="colours.abovepid" />
106                         <tocitem text="By conservation" target="colours.conservation" />
107                         <tocitem text="T-COFFEE Scores" target="io.tcoffeescores" />
108                         <tocitem text="By Annotation" target="colours.annotation" />
109                         <tocitem text="By RNA Helices" target="colours.rnahelices" />
110                 </tocitem>
111                 
112                 <tocitem text="Calculations" expand="false">
113                         <tocitem text="Sorting alignments" target="sorting" />
114                         <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
115                           <tocitem text="Calculating trees" target="trees" />
116                           <tocitem text="Principal Component Analysis" target="pca" />
117                         </tocitem>
118                         <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
119                         <tocitem text="Pairwise Alignments" target="pairwise" />
120                         <tocitem text="Remove Redundancy" target="redundancy" />
121                         <tocitem text="Reference Sequences" target="referenceseq" />
122                 </tocitem>
123                 
124                 <tocitem text="Sequence Annotations" target="seqannots" expand="true">
125                         <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
126                 </tocitem>
127                 
128                 <tocitem text="Alignment Annotations" target="alannotation" expand="false">
129                         <tocitem text="Conservation" target="calcs.alconserv" />
130                         <tocitem text="Quality" target="calcs.alquality" />
131                         <tocitem text="Consensus" target="calcs.consensus" />
132                         <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
133                         <tocitem text="Annotations File Format" target="annotations.fileformat" />
134                         <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
135                 </tocitem>
136                 <tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
137                         <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
138                         <tocitem text="PDB &amp; 3D-Beacons Structure Chooser" target="pdbchooser" />
139                         <tocitem text="Jmol Viewer" target="pdbjmol" />
140                         <tocitem text="Chimera/X Viewer" target="chimera" />
141                         <tocitem text="Pymol Viewer" target="pymol" />                  
142                 </tocitem>
143                 <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
144                 <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
145                     <tocitem text="Configuring URL Links" target="linksprefs" />
146                 </tocitem>
147                 <tocitem text="Window Menus" target="menus" expand="false">
148                         <tocitem text="Desktop Window" target="desktopMenu" />
149                         <tocitem text="Alignment Window" target="alMenu">
150                                 <tocitem text="File Menu" target="alwFile" />
151                                 <tocitem text="Edit Menu" target="alwEdit" />
152                                 <tocitem text="Select Menu" target="alwSelect" />
153                                 <tocitem text="View Menu" target="alwView" />
154                                 <tocitem text="Annotations Menu" target="alwAnnotations" />
155                                 <tocitem text="Format Menu" target="alwFormat" />
156                                 <tocitem text="Colour Menu" target="alwColour" />
157                                 <tocitem text="Calculate Menu" target="alwCalc" />
158                                 <tocitem text="Web Service Menu" target="wsMenu" />
159                                 <tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
160                                 <tocitem text="Popup Menu" target="popMenu" />
161                         </tocitem>
162                 </tocitem>
163                 <tocitem text="Preferences" target="preferences" />
164     <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
165                 <tocitem text="Scripting with Groovy" target="groovy">
166                         <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
167                 </tocitem>
168                 <tocitem text="Command Line" target="commandline" expand="false">
169                         <tocitem text="Command Line: introduction and reference" target="clarguments" />
170                         <tocitem text="Command Line: basic usage" target="clarguments-basic" />
171                         <tocitem text="Command Line: advanced usage" target="clarguments-advanced" />
172                         <tocitem text="Command Line: argument files" target="clarguments-argfiles" />
173                         <tocitem text="Command Line: reference" target="clarguments-reference" />
174                         <tocitem text="Command Line: old command line arguments" target="clarguments-old" />
175                 </tocitem>
176                 <tocitem text="Memory Settings" target="memory" expand="false"/>
177                 <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
178                 <tocitem text="Privacy" target="privacy" />
179     </tocitem>
180         <tocitem text="Useful information" expand="true">
181                 <tocitem text="Amino Acid Table" target="aminoAcids" />
182                 <tocitem text="Amino Acid Properties" target="aaProperties" />
183                 <tocitem text="The Genetic Code" target="geneticCode" />
184                 <tocitem text="Sequence Substitution Matrices" target="subtMatrices" />
185
186         </tocitem>
187 </toc>