Merge remote-tracking branch 'remotes/origin/2_5_1_rna_merge' into develop (JAL-826)

[jalview.git] / help / help.jhm

diff --git a/help/help.jhm b/help/help.jhm
index 6ed0d7b..91ef827 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -17,6 +17,7 @@
    <mapID target="msaservice" url="html/webServices/msaclient.html"/>
    <mapID target="jnet" url="html/webServices/jnet.html"/>
    <mapID target="shmrws" url="html/webServices/shmr.html"/>
+   <mapID target="newsreader" url="html/webServices/newsreader.html"/>
    <mapID target="seqfetch" url="html/features/seqfetch.html"/>
    <mapID target="dbreffetcher" url="html/webservices/dbreffetcher.html"/>
    <mapID target="seqmappings" url="html/features/seqmappings.html"/>
@@ -28,6 +29,7 @@
    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
    <mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
    <mapID target="pdbjmol" url="html/features/jmol.html"/>
+   <mapID target="varna" url="html/features/varna.html"/>
    <mapID target="preferences" url="html/features/preferences.html"/>     
    <mapID target="commandline" url="html/features/commandline.html"/>
    <mapID target="clarguments" url="html/features/clarguments.html"/>
@@ -68,11 +70,16 @@
    <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"/>
    
    <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="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"/>