X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=0c39a52a7509b1c3281a588819293160559ddef3;hb=HEAD;hp=a8ff7fa6ff991a0136b24e31c6453ef868ce7f48;hpb=e1cb1f4ff4ae05504c806d99395358629c807956;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
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--- a/help/help.jhm
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-<?xml version="1.0" encoding="ISO-8859-1" ?>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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.
--->
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-<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#Jalview.2.10.4"/>
-   <mapID target="alannotation" url="html/features/annotation.html"/>
-   <mapID target="keys" url="html/keys.html"/>
-   <mapID target="newkeys" url="html/features/newkeystrokes.html"/>
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-   <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"/>
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-   <mapID target="msaservice" url="html/webServices/msaclient.html"/>
-   <mapID target="jpred" url="html/webServices/jnet.html"/>
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-   <mapID target="aacon" url="html/webServices/AACon.html"/>
-   <mapID target="rnaalifold" url="html/webServices/RNAalifold.html"/>
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-   <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"/>
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-   <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"/>
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-   <mapID target="io.seqreport" url="html/io/exportseqreport.html"/>
-   <mapID target="io.tcoffeescores" url="html/io/tcoffeescores.html"/>
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-   <mapID target="splitframe" url="html/features/splitView.html"/>
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-   <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="backdeptextcol" url="html/colourSchemes/textcolour.html"/>
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-   <mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />
-   <mapID target="colours.taylor" url="html/colourSchemes/taylor.html" />
-   <mapID target="colours.hydro" url="html/colourSchemes/hydrophobic.html" />
-   <mapID target="colours.helix" url="html/colourSchemes/helix.html" />
-   <mapID target="colours.strand" url="html/colourSchemes/strand.html" />
-   <mapID target="colours.turn" url="html/colourSchemes/turn.html" />
-   <mapID target="colours.buried" url="html/colourSchemes/buried.html" />
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-   <mapID target="colours.user" url="html/colourSchemes/user.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"/>
-   
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-   <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
-   <mapID target="calcs.alstrconsensus" url="html/calculations/structureconsensus.html"/>  
-   <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>   
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-   
-   <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="alMenu" url="html/menus/alignmentMenu.html"/>
-   <mapID target="alwFile" url="html/menus/alwfile.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"/>
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-   <mapID target="alwColour" url="html/menus/alwcolour.html"/>
-   <mapID target="alwCalc" url="html/menus/alwcalculate.html"/>
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-   <mapID target="popMenuAddref" url="html/menus/popupMenu.html#addrefannot"/>
-   <mapID target="annotPanelMenu" url="html/menus/alwannotationpanel.html"/>
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-   <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" />
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-   <mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
-   <mapID target="pdbfts" url="html/features/pdbsequencefetcher.html#pdbfts" />
-   <mapID target="siftsmapping" url="html/features/siftsmapping.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="ensemblfetch" url="html/features/ensemblsequencefetcher.html" />
-   
-   <mapID target="uniprotfetcher" url="html/features/uniprotsequencefetcher.html" />
-   <mapID target="uniprotfts" url="html/features/uniprotsequencefetcher.html#uniprotfts" />
-   
-   <mapID target="urllinks" url="html/webServices/urllinks.html" />
-   <mapID target="linksprefs" url="html/features/preferences.html#links" />
-
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-   <mapID target="printSetupIcon" url="icons/setup.png" />
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-   <mapID target="overview" url="html/features/overview.html" />
-   <mapID target="overviewprefs" url="html/features/preferences.html#overview" />
-</map>