JAL-913; Extending documentation; VARNA help;

[jalview.git] / help / help.jhm

diff --git a/help/help.jhm b/help/help.jhm
index 056a813..3c560ab 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -11,17 +11,26 @@
    <mapID target="cursor" url="html/features/cursorMode.html"/>
    <mapID target="search" url="html/features/search.html"/>   
    <mapID target="webservice" url="html/webServices/index.html"/>
+   <mapID target="jabaws" url="html/webServices/JABAWS.html"/>
+   <mapID target="wsparams" url="html/webServices/webServicesParams.html"/>
+   <mapID target="wsprefs" url="html/webServices/webServicesPrefs.html"/>
    <mapID target="msaservice" url="html/webServices/msaclient.html"/>
    <mapID target="clustal" url="html/webServices/clustalw.html"/>
    <mapID target="muscle" url="html/webServices/muscle.html"/>
    <mapID target="mafft" url="html/webServices/mafft.html"/>
    <mapID target="jnet" url="html/webServices/jnet.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"/>
+   <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="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"/>
@@ -31,12 +40,14 @@
    <mapID target="alformats" url="html/io/fileformats.html"/>
    <mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>
    <mapID target="features.fileformat" url="html/features/featuresFormat.html"/>
+   <mapID target="features.featureschemes" url="html/features/featureschemes.html"/>
    <mapID target="das.settings" url="html/features/dassettings.html"/>
    <mapID target="das.viewing" url="html/features/dasfeatures.html"/>
    <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="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"/>
@@ -60,11 +71,16 @@
    <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"/>
@@ -82,7 +98,9 @@
    
    <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"/>
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
    <mapID target="aaProperties" url="html/misc/aaproperties.html" />
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />