documentation

[jalview.git] / help / help.jhm

diff --git a/help/help.jhm b/help/help.jhm
index 2179a73..41d245d 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -7,19 +7,27 @@
    <mapID target="release" url="html/releases.html"/>\r
    <mapID target="alannotation" url="html/features/annotation.html"/>\r
    <mapID target="keys" url="html/keys.html"/>\r
-   \r
+   <mapID target="cursor" url="html/features/cursorMode.html"/>\r
+   <mapID target="search" url="html/features/search.html"/>   \r
    <mapID target="webservice" url="html/webServices/index.html"/>\r
+   <mapID target="msaservice" url="html/webServices/msaclient.html"/>\r
    <mapID target="clustal" url="html/webServices/clustalw.html"/>\r
    <mapID target="muscle" url="html/webServices/muscle.html"/>\r
+   <mapID target="mafft" url="html/webServices/mafft.html"/>\r
    <mapID target="jnet" url="html/webServices/jnet.html"/>\r
    <mapID target="seqfetch" url="html/features/seqfetch.html"/>\r
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>\r
-   <mapID target="pdbviewer" url="html/features/pdbviewer.html"/>\r
+   <mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>\r
    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>\r
    <mapID target="preferences" url="html/features/preferences.html"/>     \r
-  <mapID target="io" url="html/io/index.html"/>\r
+   <mapID target="io" url="html/io/index.html"/>\r
+   <mapID target="io.modellerpir" url="html/io/modellerpir.html"/>\r
    <mapID target="export" url="html/io/export.html"/>\r
    <mapID target="alformats" url="html/io/fileformats.html"/>\r
+   <mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>\r
+   <mapID target="features.fileformat" url="html/features/featuresFormat.html"/>\r
+   <mapID target="das.settings" url="html/features/dassettings.html"/>\r
+   <mapID target="das.viewing" url="html/features/dasfeatures.html"/>\r
    <mapID target="edit" url="html/editing/index.html"/>\r
    <mapID target="jalarchive" url="html/features/jalarchive.html"/>\r
    <mapID target="trees" url="html/calculations/tree.html"/>\r
@@ -27,7 +35,8 @@
    <mapID target="pca" url="html/calculations/pca.html"/>\r
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>\r
    <mapID target="redundancy" url="html/calculations/redundancy.html"/>\r
-   \r
+   <mapID target="hiddenRegions" url="html/features/hiddenRegions.html"/>\r
+   <mapID target="recoverInputdata" url="html/calculations/recoverInputdata.html"/>\r
    <mapID target="colours" url="html/colourSchemes/index.html" />\r
    <mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>\r
    <mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />\r
@@ -42,12 +51,12 @@
    <mapID target="colours.pid" url="html/colourSchemes/pid.html" />\r
    <mapID target="colours.user" url="html/colourSchemes/user.html"/>\r
    <mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>\r
-   <mapID target="colours.conservation"\r
-   url="html/colourSchemes/conservation.html"/>\r
-\r
-   <mapID target="calcs.alquality"\r
-   url="html/calculations/quality.html"/>   \r
+   <mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>\r
+   <mapID target="colours.annotation" url="html/colourSchemes/annotationColouring.html"/>\r
+   \r
+   <mapID target="calcs.alquality" url="html/calculations/quality.html"/>   \r
    <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>\r
+   <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>\r
    \r
    <mapID target="menus" url="html/menus/index.html"/>\r
    <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>\r