X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=5167e2cea2609104499111e36e91bb58578dc792;hb=dc086b020537a18c3ce575fbb220033979270a65;hp=4820b6f045f639ccd07414833da15979016104d8;hpb=b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index 4820b6f..5167e2c 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -12,13 +12,16 @@
    <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="seqfetch" url="html/features/seqfetch.html"/>
+   <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
+   <mapID target="pdbviewer" url="html/features/pdbviewer.html"/>
+   <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
+   <mapID target="preferences" url="html/features/preferences.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"/>
@@ -39,7 +42,12 @@
    <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="colours.conservation"
+   url="html/colourSchemes/conservation.html"/>
+
+   <mapID target="calcs.alquality"
+   url="html/calculations/quality.html"/>   
+   <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
    
    <mapID target="menus" url="html/menus/index.html"/>
    <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
@@ -57,6 +65,7 @@
    <mapID target="memory" url="html/memory.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" />
    
    <mapID target="backIcon" url="icons/back.png" />
@@ -64,6 +73,5 @@
    <mapID target="homeIcon" url="icons/Home.png" />
    <mapID target="printIcon" url="icons/print.png" />
    <mapID target="printSetupIcon" url="icons/setup.png" />
-   <mapID target="helpIcon" url="icons/help.png" />
    
 </map>