JAL-2890 cipres example query made functional
[jalview.git] / 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>
28                 
29                 <tocitem text="Editing Alignments" target="edit" />
30                 <tocitem text="Cursor Mode" target="cursor" />
31                 <tocitem text="Key Strokes" target="keys" />
32                 
33                 <tocitem text="Input / Output" target="io" expand="false">
34                         <tocitem text="BioJSON v1.0" target="biojson" />
35                 </tocitem>
36                 
37                 <tocitem text="Making Figures" target="export" expand="false">
38                         <tocitem text="BioJS MSA Viewer" target="biojsmsa" />
39                 </tocitem>
40                 
41                 <tocitem text="Hidden Regions" target="hiddenRegions" />
42                 <tocitem text="Multiple Views" target="multipleviews" />
43                 <tocitem text="Split Frame View" target="splitframe" />
44                 <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
45                 <tocitem text="Fetching Sequences" target="seqfetch" />         
46                 
47                 <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
48                 
49                 <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
50                         <tocitem text="Viewing RNA structure" target="varna" />
51                         <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
52                         <tocitem text="RNA Helices coloring" target="colours.rnahelices" />
53                 </tocitem>
54                 
55                 <tocitem text="Sequence Features" target="seqfeatures" expand="false">
56                         <tocitem text="Sequence Feature Settings" target="seqfeatures.settings" />
57                         <tocitem text="Sequence Features File" target="features.fileformat" />
58                         <tocitem text="Feature Colourschemes" target="features.featureschemes" />
59                         <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
60                         <tocitem text="Editing Sequence Features" target="seqfeatedit" />
61                         <tocitem text="DAS Feature Retrieval" target="das.viewing" />
62                         <tocitem text="DAS Feature Settings" target="das.settings" />
63                         <tocitem text="HTML annotation report" target="io.seqreport" />
64                 </tocitem>
65                 
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" />
72                         </tocitem>
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" />
80                         <tocitem text="DAS Feature Retrieval" target="das.viewing" />
81                 </tocitem>
82                 
83                 <tocitem text="Colour Schemes" target="colours" expand="false">
84                         <tocitem text="Background Dependent Text Colour" target="backdeptextcol" />
85                         <tocitem text="ClustalX" target="colours.clustal" />
86                         <tocitem text="Zappo" target="colours.zappo" />
87                         <tocitem text="Taylor" target="colours.taylor" />
88                         <tocitem text="Hydrophobicity" target="colours.hydro" />
89                         <tocitem text="Helix propensity" target="colours.helix" />
90                         <tocitem text="Strand propensity" target="colours.strand" />
91                         <tocitem text="Turn propensity" target="colours.turn" />
92                         <tocitem text="Buried index" target="colours.buried" />
93                         <tocitem text="Nucleotide colours" target="colours.nucleotide" />
94                         <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
95                         <tocitem text="Blosum62" target="colours.blosum" />
96                         <tocitem text="by Percentage Identity" target="colours.pid" />
97                         <tocitem text="User Defined" target="colours.user" />
98                         <tocitem text="Above Percentage Identity" target="colours.abovepid" />
99                         <tocitem text="By conservation" target="colours.conservation" />
100                         <tocitem text="T-COFFEE Scores" target="io.tcoffeescores" />
101                         <tocitem text="By Annotation" target="colours.annotation" />
102                         <tocitem text="By RNA Helices" target="colours.rnahelices" />
103                 </tocitem>
104                 
105                 <tocitem text="Calculations" expand="false">
106                         <tocitem text="Sorting alignments" target="sorting" />
107                         <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
108                           <tocitem text="Calculating trees" target="trees" />
109                           <tocitem text="Principal Component Analysis" target="pca" />
110                         </tocitem>
111                         <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
112                         <tocitem text="Pairwise Alignments" target="pairwise" />
113                         <tocitem text="Remove Redundancy" target="redundancy" />
114                         <tocitem text="Reference Sequences" target="referenceseq" />
115                 </tocitem>
116                 
117                 <tocitem text="Sequence Annotations" target="seqannots" expand="true">
118                         <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
119                 </tocitem>
120                 
121                 <tocitem text="Alignment Annotations" target="alannotation" expand="false">
122                         <tocitem text="Conservation" target="calcs.alconserv" />
123                         <tocitem text="Quality" target="calcs.alquality" />
124                         <tocitem text="Consensus" target="calcs.consensus" />
125                         <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
126                         <tocitem text="Annotations File Format" target="annotations.fileformat" />
127                         <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
128                 </tocitem>
129                 <tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
130                         <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
131                         <tocitem text="PDB Structure Chooser" target="pdbchooser" />
132                         <tocitem text="Jmol Viewer" target="pdbjmol" />
133                         <tocitem text="Chimera Viewer" target="chimera" />                      
134                 </tocitem>
135                 <tocitem text="Viewing RNA structures" target="varna" expand="false"/>
136                 <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
137                     <tocitem text="Configuring URL Links" target="linksprefs" />
138                 </tocitem>
139                 <tocitem text="VAMSAS Data Exchange" target="vamsas">
140                         <!-- what can Jalview share with other apps -->
141                         <!-- what other apps exist -->
142                 </tocitem>
143                 <tocitem text="Window Menus" target="menus" expand="false">
144                         <tocitem text="Desktop Window" target="desktopMenu" />
145                         <tocitem text="Alignment Window" target="alMenu">
146                                 <tocitem text="File Menu" target="alwFile" />
147                                 <tocitem text="Edit Menu" target="alwEdit" />
148                                 <tocitem text="Select Menu" target="alwSelect" />
149                                 <tocitem text="View Menu" target="alwView" />
150                                 <tocitem text="Annotations Menu" target="alwAnnotations" />
151                                 <tocitem text="Format Menu" target="alwFormat" />
152                                 <tocitem text="Colour Menu" target="alwColour" />
153                                 <tocitem text="Calculate Menu" target="alwCalc" />
154                                 <tocitem text="Web Service Menu" target="wsMenu" />
155                                 <tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
156                                 <tocitem text="Popup Menu" target="popMenu" />
157                         </tocitem>
158                 </tocitem>
159                 <tocitem text="Preferences" target="preferences" />
160                 <tocitem text="Memory Settings" target="memory" expand="false"/>
161                 <tocitem text="Scripting with Groovy" target="groovy">
162                         <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
163                 </tocitem>
164                 <tocitem text="Command Line" target="commandline" expand="false">
165                         <tocitem text="Command Line Arguments" target="clarguments" />
166                 </tocitem>
167                 <tocitem text="Privacy" target="privacy" />
168         </tocitem>
169         <tocitem text="Useful information" expand="true">
170                 <tocitem text="Amino Acid Table" target="aminoAcids" />
171                 <tocitem text="Amino Acid Properties" target="aaProperties" />
172                 <tocitem text="The Genetic Code" target="geneticCode" />
173                 <tocitem text="Sequence Substitution Matrices" target="subtMatrices" />
174
175         </tocitem>
176 </toc>