X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=7e14204cfc78dc5928d298e832735dd12408f891;hb=b7ac40022712978f3a452b30d7d2fe9288f18613;hp=af010a49bd99242576616ca4bc4df356992543e2;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index af010a4..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"/>
@@ -74,12 +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"/>
@@ -105,7 +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"/>
    
@@ -128,6 +130,7 @@
    
    <mapID target="memory" url="html/memory.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" />
@@ -136,6 +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" />