X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=7e14204cfc78dc5928d298e832735dd12408f891;hb=894672b99c68bc0562ef5a3a0396a4825c8d7d48;hp=b199dbfd8a39cfdb99eb729a2d17a6306ccb3489;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index b199dbf..7e14204 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1" ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,7 +22,7 @@
    <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"/>
@@ -39,6 +39,7 @@
    <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"/>
@@ -52,8 +53,11 @@
    <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"/>
@@ -70,12 +74,14 @@
    <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"/>
@@ -101,7 +107,7 @@
    <mapID target="calcs.alquality" url="html/calculations/quality.html"/>   
    <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"/>
+   <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>   
    
    <mapID target="nucleicAcids" url="html/na/index.html"/>
    
@@ -112,17 +118,19 @@
    <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="groovy.featurecounter" url="html/groovy/featureCounter.html" />
    <mapID target="privacy" url="html/privacy.html" />
    <mapID target="vamsas" url="html/vamsas/index.html"/>
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
@@ -131,6 +139,17 @@
    <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="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="backIcon" url="icons/back.png" />
    <mapID target="forwardIcon" url="icons/forward.png" />
    <mapID target="homeIcon" url="icons/Home.png" />