X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=16e620f28742b1d5c43bc527b66361089ca4cc94;hb=69e9cd54dcfd25dd3067f353bc53eb6b4d7e27af;hp=2a479e9d6dbeb0237f40992ddfaf65ae29ee8faa;hpb=4e377b5c02352a12537100dddd2f8a2b84536205;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index 2a479e9..16e620f 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -8,20 +8,25 @@
    <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="jnet" url="html/webServices/jnet.html"/>
    <mapID target="seqfetch" url="html/features/seqfetch.html"/>
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
+   <mapID target="seqfeatures.settings" url="html/features/featuresettings.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="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="edit" url="html/editing/index.html"/>
+   <mapID target="edit.selareas" url="html/editing/selectionAreas.html"/>
    <mapID target="jalarchive" url="html/features/jalarchive.html"/>
    <mapID target="trees" url="html/calculations/tree.html"/>
    <mapID target="sorting" url="html/calculations/sorting.html"/>
@@ -45,9 +50,8 @@
    <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.alquality" url="html/calculations/quality.html"/>   
    <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
    
    <mapID target="menus" url="html/menus/index.html"/>