X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp.jhm;h=41d245d383e7e356534b3fd12d273411ece600ab;hb=d1adb73839eeca1210d755c725bd625a0c2b9067;hp=2dff0de026784a8a19fda8222cd88504538a22e9;hpb=cb8ec179c020265666678572815ab056a024da22;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index 2dff0de..41d245d 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -8,19 +8,26 @@
    <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="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="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"/>
@@ -28,7 +35,8 @@
    <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="recoverInputdata" url="html/calculations/recoverInputdata.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" />
@@ -45,9 +53,10 @@
    <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"/>