X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=2cfe8d826937c7316717f14910fb0aedcfc58c28;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=9560ecfdec5957c7dc395a2bac7db45229ef9f28;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index 9560ecf..2cfe8d8 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -1,20 +1,21 @@
 <?xml version="1.0" encoding="ISO-8859-1" ?>
 <!--
-  Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
-  Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-  
-  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/>.
+ * 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.
 -->
    <!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">
@@ -37,19 +38,26 @@
    <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="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"/>
@@ -97,7 +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"/>
    
@@ -108,16 +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"/>
@@ -125,6 +135,7 @@
    <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="backIcon" url="icons/back.png" />
    <mapID target="forwardIcon" url="icons/forward.png" />