Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git] / help / help / help.jhm
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 of the License, or (at your option) any later version.
11  *  
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.
16  * 
17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
18  * The Jalview Authors are detailed in the 'AUTHORS' file.
19 -->
20    <!DOCTYPE map PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Map Version 1.0//EN" "http://java.sun.com/products/javahelp/map_1_0.dtd">
21 <map version="1.0">
22    <mapID target="home" url="html/index.html" />
23    
24    <mapID target="new" url="html/whatsNew.html"/>
25    <mapID target="release" url="html/releases.html#Jalview.$$Version-Rel$$"/>
26    <mapID target="alannotation" url="html/features/annotation.html"/>
27    <mapID target="keys" url="html/keys.html"/>
28    <mapID target="newkeys" url="html/features/newkeystrokes.html"/>
29    <mapID target="cursor" url="html/features/cursorMode.html"/>
30    <mapID target="search" url="html/features/search.html"/>   
31    <mapID target="webservice" url="html/webServices/index.html"/>
32    <mapID target="jabaws" url="html/webServices/JABAWS.html"/>
33    <mapID target="wsparams" url="html/webServices/webServicesParams.html"/>
34    <mapID target="wsprefs" url="html/webServices/webServicesPrefs.html"/>
35    <mapID target="msaservice" url="html/webServices/msaclient.html"/>
36    <mapID target="jpred" url="html/webServices/jnet.html"/>
37    <mapID target="shmrws" url="html/webServices/shmr.html"/>
38    <mapID target="newsreader" url="html/webServices/newsreader.html"/>
39    <mapID target="disorder" url="html/webServices/proteinDisorder.html"/>
40    <mapID target="aacon" url="html/webServices/AACon.html"/>
41    <mapID target="rnaalifold" url="html/webServices/RNAalifold.html"/>
42    <mapID target="seqannots" url="html/features/annotation.html#seqannots"/>
43    <mapID target="seqfetch" url="html/features/seqfetch.html"/>
44    <mapID target="dbreffetcher" url="html/webServices/dbreffetcher.html"/>
45    <mapID target="seqmappings" url="html/features/seqmappings.html"/>
46    <mapID target="cdnafeatures" url="html/features/codingfeatures.html"/>
47    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
48    <mapID target="seqfeatedit" url="html/features/editingFeatures.html"/>
49    <mapID target="seqfeatcreat" url="html/features/creatinFeatures.html"/>
50    <mapID target="seqfeatures.report" url="html/features/seqfeaturereport.html"/>
51    <mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
52    <mapID target="seqfeatures.settings.selcols" url="html/features/featuresettings.html#selectbyfeature"/>
53    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
54    <mapID target="viewingpdbs.reps" url="html/features/viewingpdbs.html#viewreps"/>
55    <mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
56    <mapID target="pdbjmol" url="html/features/jmol.html"/>
57    <mapID target="chimera" url="html/features/chimera.html"/>
58    <mapID target="pymol" url="html/features/pymol.html"/>
59    <mapID target="chimera.annotxfer" url="html/features/chimera.html#annotxfer"/>
60    <mapID target="varna" url="html/features/varna.html"/>
61    <mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
62    <mapID target="preferences" url="html/features/preferences.html"/>     
63    <mapID target="startupprefs" url="html/features/preferences.html#startup"/>     
64    <mapID target="strucprefs" url="html/features/preferences.html#structure"/>     
65    <mapID target="commandline" url="html/features/commandline.html"/>
66    <mapID target="jalviewcltool" url="html/features/commandline.html#script"/>
67    <mapID target="clarguments" url="html/features/clarguments.html"/>
68    <mapID target="jvlfiles" url="html/features/jvlfiles.html"/>
69    <mapID target="io" url="html/io/index.html"/>
70    <mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
71    <mapID target="io.seqreport" url="html/io/exportseqreport.html"/>
72    <mapID target="io.tcoffeescores" url="html/io/tcoffeescores.html"/>
73    <mapID target="export" url="html/io/export.html"/>
74    <mapID target="alformats" url="html/io/fileformats.html"/>
75    <mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>
76    <mapID target="features.fileformat" url="html/features/featuresFormat.html"/>
77    <mapID target="features.featureschemes" url="html/features/featureschemes.html"/>
78    <mapID target="edit" url="html/editing/index.html"/>
79    <mapID target="jalarchive" url="html/features/jalarchive.html"/>
80    <mapID target="multipleviews" url="html/features/multipleViews.html"/>
81    <mapID target="splitframe" url="html/features/splitView.html"/>
82    <mapID target="splitframe.virtualfeats" url="html/features/splitView.html#virtualfeats"/>
83    <mapID target="splitframe.mirrorfonts" url="html/features/splitView.html#mirror"/>
84    <mapID target="trees" url="html/calculations/tree.html"/>
85    <mapID target="treeviewer" url="html/calculations/treeviewer.html"/>
86    <mapID target="sorting" url="html/calculations/sorting.html"/>
87    <mapID target="pca" url="html/calculations/pca.html"/>
88    <mapID target="pairwise" url="html/calculations/pairwise.html"/>
89    <mapID target="redundancy" url="html/calculations/redundancy.html"/>
90    <mapID target="referenceseq" url="html/calculations/referenceseq.html"/>
91    <mapID target="hiddenRegions" url="html/features/hiddenRegions.html"/>
92    <mapID target="recoverInputdata" url="html/calculations/recoverInputdata.html"/>
93    <mapID target="colours" url="html/colourSchemes/index.html"/>
94    <mapID target="backdeptextcol" url="html/colourSchemes/textcolour.html"/>
95    <mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>
96    <mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />
97    <mapID target="colours.taylor" url="html/colourSchemes/taylor.html" />
98    <mapID target="colours.gecos-flower" url="html/colourSchemes/gecos-flower.html" />
99    <mapID target="colours.gecos-blossom" url="html/colourSchemes/gecos-blossom.html" />
100    <mapID target="colours.gecos-sunset" url="html/colourSchemes/gecos-sunset.html" />
101    <mapID target="colours.gecos-ocean" url="html/colourSchemes/gecos-ocean.html" />
102    <mapID target="colours.hydro" url="html/colourSchemes/hydrophobic.html" />
103    <mapID target="colours.helix" url="html/colourSchemes/helix.html" />
104    <mapID target="colours.strand" url="html/colourSchemes/strand.html" />
105    <mapID target="colours.turn" url="html/colourSchemes/turn.html" />
106    <mapID target="colours.buried" url="html/colourSchemes/buried.html" />
107    <mapID target="colours.nucleotide" url="html/colourSchemes/nucleotide.html" />
108    <mapID target="colours.blosum" url="html/colourSchemes/blosum.html" />
109    <mapID target="colours.pid" url="html/colourSchemes/pid.html" />
110    <mapID target="colours.user" url="html/colourSchemes/user.html"/>
111    <mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>
112    <mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>
113    <mapID target="colours.annotation" url="html/colourSchemes/annotationColouring.html"/>
114    <mapID target="colours.purinepyrimidine" url="html/colourSchemes/purinepyrimidine.html"/>
115    <mapID target="colours.rnahelices" url="html/colourSchemes/rnahelicesColouring.html"/>
116    
117    <mapID target="calcs.alquality" url="html/calculations/quality.html"/>   
118    <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
119    <mapID target="calcs.alstrconsensus" url="html/calculations/structureconsensus.html"/>  
120    <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>   
121    <mapID target="calcs.dialog" url="html/calculations/calculations.html"/>
122    
123    <mapID target="nucleicAcids" url="html/na/index.html"/>
124    
125    <mapID target="menus" url="html/menus/index.html"/>
126    <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
127    <mapID target="alMenu" url="html/menus/alignmentMenu.html"/>
128    <mapID target="alwFile" url="html/menus/alwfile.html"/>
129    <mapID target="alwEdit" url="html/menus/alwedit.html"/>
130    <mapID target="alwSelect" url="html/menus/alwselect.html"/>
131    <mapID target="alwView" url="html/menus/alwview.html"/>
132    <mapID target="alwAnnotations" url="html/menus/alwannotation.html"/>
133    <mapID target="alwFormat" url="html/menus/alwformat.html"/>
134    <mapID target="alwColour" url="html/menus/alwcolour.html"/>
135    <mapID target="alwCalc" url="html/menus/alwcalculate.html"/>
136    
137    <mapID target="wsMenu" url="html/menus/wsmenu.html"/>
138    <mapID target="alwHmmer" url="html/menus/alwhmmer.html"/>
139    <mapID target="popMenu" url="html/menus/popupMenu.html"/>
140    <mapID target="popMenuAddref" url="html/menus/popupMenu.html#addrefannot"/>
141    <mapID target="annotPanelMenu" url="html/menus/alwannotationpanel.html"/>
142    
143    <mapID target="memory" url="html/memory.html" />
144    <mapID target="groovy" url="html/features/groovy.html" />
145    <mapID target="groovy.colours" url="html/features/groovy.html#groovyColours" />
146    <mapID target="groovy.featurescounter" url="html/groovy/featuresCounter.html" />
147    <mapID target="privacy" url="html/privacy.html" />
148    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
149    <mapID target="aaProperties" url="html/misc/aaproperties.html" />
150    <mapID target="geneticCode" url="html/misc/geneticCode.html" />
151    <mapID target="subtMatrices" url="html/calculations/scorematrices.html" />
152    <mapID target="subtMatrices.pam250" url="html/calculations/scorematrices.html#pam250" />
153    
154    <mapID target="biojson" url="html/features/bioJsonFormat.html" />
155    <mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
156    <mapID target="pdbfts" url="html/features/pdbsequencefetcher.html#pdbfts" />
157    <mapID target="siftsmapping" url="html/features/siftsmapping.html" />
158    <mapID target="pdbchooser" url="html/features/structurechooser.html" />
159    <mapID target="structuresvia3dbeacons" url="html/features/structurechooser.html#3dbeaconssearch" />   
160    <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
161    <mapID target="biojsmsa" url="html/features/biojsmsa.html" />
162    
163    <mapID target="ensemblfetch" url="html/features/ensemblsequencefetcher.html" />
164    
165    <mapID target="uniprotfetcher" url="html/features/uniprotsequencefetcher.html" />
166    <mapID target="uniprotfts" url="html/features/uniprotsequencefetcher.html#uniprotfts" />
167    
168    <mapID target="urllinks" url="html/webServices/urllinks.html" />
169    <mapID target="linksprefs" url="html/features/preferences.html#links" />
170
171    <mapID target="backIcon" url="icons/back.png" />
172    <mapID target="forwardIcon" url="icons/forward.png" />
173    <mapID target="homeIcon" url="icons/Home.png" />
174    <mapID target="printIcon" url="icons/print.png" />
175    <mapID target="printSetupIcon" url="icons/setup.png" />
176    
177    <mapID target="overview" url="html/features/overview.html" />
178    <mapID target="overviewprefs" url="html/features/preferences.html#overview" />
179    
180    <mapID target="importvcf" url="html/features/importvcf.html" />
181    <mapID target="importvcf.attribs" url="html/features/importvcf.html#attribs" />
182    <mapID target="logging" url="html/logging.html" />
183 </map>