<?xml version="1.0" encoding="ISO-8859-1" ?>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
<!DOCTYPE map PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Map Version 1.0//EN" "http://java.sun.com/products/javahelp/map_1_0.dtd">
<map version="1.0">
<mapID target="home" url="html/index.html" />
<mapID target="new" url="html/whatsNew.html"/>
- <mapID target="release" url="html/releases.html"/>
+ <mapID target="release" url="html/releases.html#Jalview.2.9"/>
<mapID target="alannotation" url="html/features/annotation.html"/>
<mapID target="keys" url="html/keys.html"/>
<mapID target="newkeys" url="html/features/newkeystrokes.html"/>
<mapID target="cursor" url="html/features/cursorMode.html"/>
<mapID target="search" url="html/features/search.html"/>
<mapID target="webservice" url="html/webServices/index.html"/>
+ <mapID target="jabaws" url="html/webServices/JABAWS.html"/>
+ <mapID target="wsparams" url="html/webServices/webServicesParams.html"/>
+ <mapID target="wsprefs" url="html/webServices/webServicesPrefs.html"/>
<mapID target="msaservice" url="html/webServices/msaclient.html"/>
- <mapID target="clustal" url="html/webServices/clustalw.html"/>
- <mapID target="muscle" url="html/webServices/muscle.html"/>
- <mapID target="mafft" url="html/webServices/mafft.html"/>
<mapID target="jnet" url="html/webServices/jnet.html"/>
+ <mapID target="shmrws" url="html/webServices/shmr.html"/>
+ <mapID target="newsreader" url="html/webServices/newsreader.html"/>
+ <mapID target="disorder" url="html/webServices/proteinDisorder.html"/>
+ <mapID target="aacon" url="html/webServices/AACon.html"/>
+ <mapID target="rnaalifold" url="html/webServices/RNAalifold.html"/>
+ <mapID target="seqannots" url="html/features/annotation.html#seqannots"/>
<mapID target="seqfetch" url="html/features/seqfetch.html"/>
+ <mapID target="dbreffetcher" url="html/webServices/dbreffetcher.html"/>
<mapID target="seqmappings" url="html/features/seqmappings.html"/>
<mapID target="cdnafeatures" url="html/features/codingfeatures.html"/>
<mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
<mapID target="seqfeatedit" url="html/features/editingFeatures.html"/>
<mapID target="seqfeatcreat" url="html/features/creatinFeatures.html"/>
<mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
+ <mapID target="seqfeatures.settings.selcols" url="html/features/featuresettings.html#selectbyfeature"/>
<mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
+ <mapID target="viewingpdbs.reps" url="html/features/viewingpdbs.html#viewreps"/>
+ <mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
+ <mapID target="pdbjmol" url="html/features/jmol.html"/>
+ <mapID target="chimera" url="html/features/chimera.html"/>
+ <mapID target="varna" url="html/features/varna.html"/>
+ <mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
<mapID target="preferences" url="html/features/preferences.html"/>
+ <mapID target="strucprefs" url="html/features/preferences.html#structure"/>
<mapID target="commandline" url="html/features/commandline.html"/>
<mapID target="clarguments" url="html/features/clarguments.html"/>
<mapID target="io" url="html/io/index.html"/>
<mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
+ <mapID target="io.seqreport" url="html/io/exportseqreport.html"/>
+ <mapID target="io.tcoffeescores" url="html/io/tcoffeescores.html"/>
<mapID target="export" url="html/io/export.html"/>
<mapID target="alformats" url="html/io/fileformats.html"/>
<mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>
<mapID target="features.fileformat" url="html/features/featuresFormat.html"/>
+ <mapID target="features.featureschemes" url="html/features/featureschemes.html"/>
<mapID target="das.settings" url="html/features/dassettings.html"/>
<mapID target="das.viewing" url="html/features/dasfeatures.html"/>
<mapID target="edit" url="html/editing/index.html"/>
<mapID target="jalarchive" url="html/features/jalarchive.html"/>
<mapID target="multipleviews" url="html/features/multipleViews.html"/>
+ <mapID target="splitframe" url="html/features/splitView.html"/>
<mapID target="trees" url="html/calculations/tree.html"/>
+ <mapID target="treeviewer" url="html/calculations/treeviewer.html"/>
<mapID target="sorting" url="html/calculations/sorting.html"/>
<mapID target="pca" url="html/calculations/pca.html"/>
<mapID target="pairwise" url="html/calculations/pairwise.html"/>
<mapID target="redundancy" url="html/calculations/redundancy.html"/>
+ <mapID target="referenceseq" url="html/calculations/referenceseq.html"/>
<mapID target="hiddenRegions" url="html/features/hiddenRegions.html"/>
<mapID target="recoverInputdata" url="html/calculations/recoverInputdata.html"/>
<mapID target="colours" url="html/colourSchemes/index.html"/>
<mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>
<mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>
<mapID target="colours.annotation" url="html/colourSchemes/annotationColouring.html"/>
+ <mapID target="colours.purinepyrimidine" url="html/colourSchemes/purinepyrimidine.html"/>
+ <mapID target="colours.rnahelices" url="html/colourSchemes/rnahelicesColouring.html"/>
<mapID target="calcs.alquality" url="html/calculations/quality.html"/>
<mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
- <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>
+ <mapID target="calcs.alstrconsensus" url="html/calculations/structureconsensus.html"/>
+ <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>
+
+ <mapID target="nucleicAcids" url="html/na/index.html"/>
<mapID target="menus" url="html/menus/index.html"/>
<mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
<mapID target="alwEdit" url="html/menus/alwedit.html"/>
<mapID target="alwSelect" url="html/menus/alwselect.html"/>
<mapID target="alwView" url="html/menus/alwview.html"/>
+ <mapID target="alwAnnotations" url="html/menus/alwannotation.html"/>
<mapID target="alwFormat" url="html/menus/alwformat.html"/>
<mapID target="alwColour" url="html/menus/alwcolour.html"/>
<mapID target="alwCalc" url="html/menus/alwcalculate.html"/>
<mapID target="wsMenu" url="html/menus/wsmenu.html"/>
<mapID target="popMenu" url="html/menus/popupMenu.html"/>
- <mapID target="annotMenus" url="html/menus/alwannotations.html"/>
+ <mapID target="popMenuAddref" url="html/menus/popupMenu.html#addrefannot"/>
+ <mapID target="annotPanelMenu" url="html/menus/alwannotationpanel.html"/>
<mapID target="memory" url="html/memory.html" />
- <mapID target="jalviewjnlp" url="html/jalviewjnlp.html" />
-
+ <mapID target="groovy" url="html/features/groovy.html" />
+ <mapID target="privacy" url="html/privacy.html" />
+ <mapID target="vamsas" url="html/vamsas/index.html"/>
<mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
<mapID target="aaProperties" url="html/misc/aaproperties.html" />
<mapID target="geneticCode" url="html/misc/geneticCode.html" />
+ <mapID target="subtMatrices" url="html/calculations/scorematrices.html" />
+ <mapID target="subtMatrices.pam250" url="html/calculations/scorematrices.html#pam250" />
+
+ <mapID target="biojson" url="html/features/bioJsonFormat.html" />
+ <mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
+ <mapID target="pdbchooser" url="html/features/structurechooser.html" />
+ <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
+ <mapID target="biojsmsa" url="html/features/biojsmsa.html" />
<mapID target="backIcon" url="icons/back.png" />
<mapID target="forwardIcon" url="icons/forward.png" />
git://source.jalview.org / jalview.git / blobdiff