X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp.jhm;h=8c314d33ddf84d16e85359111617564753526903;hb=0ae0d247aec4361dc0a743d10abd3e9743d6c180;hp=231bcbc6188ac80a10102362e692bb7d974d3141;hpb=b785060f71751dd08fced2b4c84c9efcab62ac0e;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index 231bcbc..8c314d3 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -7,19 +7,26 @@
    <mapID target="release" url="html/releases.html"/>
    <mapID target="alannotation" url="html/features/annotation.html"/>
    <mapID target="keys" url="html/keys.html"/>
-   
+   <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="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="seqfeatures" url="html/features/seqfeatures.html"/>
-   <mapID target="pdbviewer" url="html/features/pdbviewer.html"/>
+   <mapID target="seqfeatures.settings" url="html/features/featuresettings.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="io" url="html/io/index.html"/>
+   <mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
    <mapID target="export" url="html/io/export.html"/>
    <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="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="trees" url="html/calculations/tree.html"/>
@@ -27,6 +34,7 @@
    <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="hiddenRegions" url="html/features/hiddenRegions.html"/>
    
    <mapID target="colours" url="html/colourSchemes/index.html" />
    <mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>
@@ -43,6 +51,11 @@
    <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.annotation" url="html/colourSchemes/annotationColouring.html"/>
+   
+   <mapID target="calcs.alquality" url="html/calculations/quality.html"/>   
+   <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
+   <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>
    
    <mapID target="menus" url="html/menus/index.html"/>
    <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
@@ -58,6 +71,7 @@
    <mapID target="annotMenus" url="html/menus/alwannotations.html"/>
    
    <mapID target="memory" url="html/memory.html" />
+   <mapID target="jalviewjnlp" url="html/jalviewjnlp.html" />
    
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
    <mapID target="aaProperties" url="html/misc/aaproperties.html" />