X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=2cfe8d826937c7316717f14910fb0aedcfc58c28;hb=b6d073bedc4b28e1a0e5a3a899cfb0e32349087e;hp=cc272e8e3338949f21307bb71081cf67b2a4d5b2;hpb=7a75fae1d4cc6136494716bfaa2b1edb26ca76be;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index cc272e8..2cfe8d8 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 2.8.1)
- * 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.
  * 
@@ -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"/>
@@ -49,10 +50,14 @@
    <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"/>
@@ -100,7 +105,8 @@
    <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="calcs.annotation" url="html/calculations/columnFilterByAnnotation.html"/>
    
    <mapID target="nucleicAcids" url="html/na/index.html"/>
    
@@ -111,16 +117,17 @@
    <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"/>