X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=7d884b378be06ca85d245e162e391688a8abb294;hb=246746e55bd02c66746d5cd872f49890cbae206a;hp=363ee887945367cb72d94644d7a1738e37c235f6;hpb=bfbc6adb2123ba3e4c267384c0d39849f888c794;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index 363ee88..7d884b3 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -3,19 +3,58 @@
 <map version="1.0">
    <mapID target="home" url="html/index.html" />
    
-   <mapID target="calculate" url="html/menus/calculateMenu.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="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="alannotation" url="html/features/annotation.html"/>
+   
+   <mapID target="webservice" url="html/webServices/index.html"/>
+   <mapID target="clustal" url="html/webServices/clustalw.html"/>
+   <mapID target="muscle" url="html/webServices/muscle.html"/>
+   <mapID target="jnet" url="html/webServices/jnet.html"/>
+   
+   <mapID target="io" url="html/io/index.html"/>
+   <mapID target="export" url="html/io/export.html"/>
+   <mapID target="alformats" url="html/io/fileformats.html"/>
+   <mapID target="edit" url="html/editing/index.html"/>
+   <mapID target="jalarchive" url="html/features/jalarchive.html"/>
+   <mapID target="calculations" url="html/calculations/index.html"/>
+   <mapID target="trees" url="html/calculations/tree.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"/>
+   <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="menus" url="html/menus/index.html"/>
+   <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
+   <mapID target="alMenu" url="html/menus/alignmentMenu.html"/>
+   <mapID target="alwFile" url="html/menus/alwfile.html"/>
+   <mapID target="alwEdit" url="html/menus/alwedit.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="aminoAcids" url="html/misc/aminoAcids.html" />
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />