X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=627a8c0aa5820b12a85e35e5502c7c0d7dc6b238;hb=6fa9683bef52d6709abb81840681e4fa452cafe7;hp=363ee887945367cb72d94644d7a1738e37c235f6;hpb=bfbc6adb2123ba3e4c267384c0d39849f888c794;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index 363ee88..627a8c0 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -2,20 +2,41 @@
    <!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">
    <mapID target="home" url="html/index.html" />
+   <mapID target="start" url="html/start.html"/>
    
-   <mapID target="calculate" url="html/menus/calculateMenu.html" />
+   <mapID target="new" url="html/whatsNew.html"/>
+   <mapID target="search" url="html/features/search.html"/>
+   <mapID target="wrap" url="html/features/wrap.html"/>
+   <mapID target="overview" url="html/features/overview.html"/>
+   <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
    
-   <mapID target="colours" url="html/colourSchemes/colourSchemes.html" />
-   <mapID target="colours.zappo" url="html/colourSchemes/colourSchemes.html#zappo" />
-   <mapID target="colours.taylor" url="html/colourSchemes/colourSchemes.html#taylor" />
-   <mapID target="colours.hydro" url="html/colourSchemes/colourSchemes.html#hydrophobic" />
-   <mapID target="colours.helix" url="html/colourSchemes/colourSchemes.html#helix" />
-   <mapID target="colours.strand" url="html/colourSchemes/colourSchemes.html#strand" />
-   <mapID target="colours.turn" url="html/colourSchemes/colourSchemes.html#turn" />
-   <mapID target="colours.buried" url="html/colourSchemes/colourSchemes.html#buried" />
-   <mapID target="colours.nucleotide" url="html/colourSchemes/colourSchemes.html#nucleotide" />
-   <mapID target="colours.blosum" url="html/colourSchemes/colourSchemes.html#blosum" />
-   <mapID target="colours.pid" url="html/colourSchemes/colourSchemes.html#pid" />
+   <mapID target="webservice" url="html/webServices/index.html"/>
+   <mapID target="clustal" url="html/webServices/clustal.html"/>
+   
+   <mapID target="io" url="html/io/index.html"/>
+   <mapID target="edit" url="html/editing/index.html"/>
+   
+   <mapID target="trees" url="html/calculations/tree.html"/>
+   <mapID target="conservation" url="html/calculations/conservation.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="colours" url="html/colourSchemes/index.html" />
+   <mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>
+   <mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />
+   <mapID target="colours.taylor" url="html/colourSchemes/taylor.html" />
+   <mapID target="colours.hydro" url="html/colourSchemes/hydrophobic.html" />
+   <mapID target="colours.helix" url="html/colourSchemes/helix.html" />
+   <mapID target="colours.strand" url="html/colourSchemes/strand.html" />
+   <mapID target="colours.turn" url="html/colourSchemes/turn.html" />
+   <mapID target="colours.buried" url="html/colourSchemes/buried.html" />
+   <mapID target="colours.nucleotide" url="html/colourSchemes/nucleotide.html" />
+   <mapID target="colours.blosum" url="html/colourSchemes/blosum.html" />
+   <mapID target="colours.pid" url="html/colourSchemes/pid.html" />
+   <mapID target="colours.user" url="html/colourSchemes/user.html"/>
+   <mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>
+   <mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>
    
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />