added the sorting entry to calculations, and corrected the PID

[jalview.git] / help / help.jhm

diff --git a/help/help.jhm b/help/help.jhm
index 363ee88..36a54e4 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -3,19 +3,46 @@
 <map version="1.0">\r
    <mapID target="home" url="html/index.html" />\r
    \r
-   <mapID target="calculate" url="html/menus/calculateMenu.html" />\r
-   \r
-   <mapID target="colours" url="html/colourSchemes/colourSchemes.html" />\r
-   <mapID target="colours.zappo" url="html/colourSchemes/colourSchemes.html#zappo" />\r
-   <mapID target="colours.taylor" url="html/colourSchemes/colourSchemes.html#taylor" />\r
-   <mapID target="colours.hydro" url="html/colourSchemes/colourSchemes.html#hydrophobic" />\r
-   <mapID target="colours.helix" url="html/colourSchemes/colourSchemes.html#helix" />\r
-   <mapID target="colours.strand" url="html/colourSchemes/colourSchemes.html#strand" />\r
-   <mapID target="colours.turn" url="html/colourSchemes/colourSchemes.html#turn" />\r
-   <mapID target="colours.buried" url="html/colourSchemes/colourSchemes.html#buried" />\r
-   <mapID target="colours.nucleotide" url="html/colourSchemes/colourSchemes.html#nucleotide" />\r
-   <mapID target="colours.blosum" url="html/colourSchemes/colourSchemes.html#blosum" />\r
-   <mapID target="colours.pid" url="html/colourSchemes/colourSchemes.html#pid" />\r
+   <mapID target="new" url="html/whatsNew.html"/>\r
+   <mapID target="search" url="html/features/search.html"/>\r
+   <mapID target="wrap" url="html/features/wrap.html"/>\r
+   <mapID target="overview" url="html/features/overview.html"/>\r
+   <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>\r
+   \r
+   <mapID target="webservice" url="html/webServices/index.html"/>\r
+   <mapID target="clustal" url="html/webServices/clustal.html"/>\r
+   \r
+   <mapID target="io" url="html/io/index.html"/>\r
+   <mapID target="edit" url="html/editing/index.html"/>\r
+\r
+   <mapID target="calculations" url="html/calculations/index.html"/>\r
+   <mapID target="trees" url="html/calculations/tree.html"/>\r
+   <mapID target="sorting" url="html/calculations/sorting.html"/>\r
+   <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="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
+   <mapID target="colours.taylor" url="html/colourSchemes/taylor.html" />\r
+   <mapID target="colours.hydro" url="html/colourSchemes/hydrophobic.html" />\r
+   <mapID target="colours.helix" url="html/colourSchemes/helix.html" />\r
+   <mapID target="colours.strand" url="html/colourSchemes/strand.html" />\r
+   <mapID target="colours.turn" url="html/colourSchemes/turn.html" />\r
+   <mapID target="colours.buried" url="html/colourSchemes/buried.html" />\r
+   <mapID target="colours.nucleotide" url="html/colourSchemes/nucleotide.html" />\r
+   <mapID target="colours.blosum" url="html/colourSchemes/blosum.html" />\r
+   <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" url="html/colourSchemes/conservation.html"/>\r
+   \r
+   <mapID target="menus" url="html/menus/index.html"/>\r
+   <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>\r
+   <mapID target="alMenu" url="html/menus/alignmentMenu.html"/>\r
+   <mapID target="popMenu" url="html/menus/popupMenu.html"/>\r
+   \r
    \r
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />\r
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />\r