AA properties added

[jalview.git] / help / help.jhm

diff --git a/help/help.jhm b/help/help.jhm
index 363ee88..231bcbc 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -3,21 +3,70 @@
 <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="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="webservice" url="html/webServices/index.html"/>\r
+   <mapID target="clustal" url="html/webServices/clustalw.html"/>\r
+   <mapID target="muscle" url="html/webServices/muscle.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="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="export" url="html/io/export.html"/>\r
+   <mapID target="alformats" url="html/io/fileformats.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
+   <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="alwFile" url="html/menus/alwfile.html"/>\r
+   <mapID target="alwEdit" url="html/menus/alwedit.html"/>\r
+   <mapID target="alwView" url="html/menus/alwview.html"/>\r
+   <mapID target="alwColour" url="html/menus/alwcolour.html"/>\r
+   <mapID target="alwCalc" url="html/menus/alwcalculate.html"/>\r
+   \r
+   <mapID target="wsMenu" url="html/menus/wsmenu.html"/>\r
+   <mapID target="popMenu" url="html/menus/popupMenu.html"/>\r
+   <mapID target="annotMenus" url="html/menus/alwannotations.html"/>\r
+   \r
+   <mapID target="memory" url="html/memory.html" />\r
    \r
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />\r
+   <mapID target="aaProperties" url="html/misc/aaproperties.html" />\r
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />\r
    \r
+   <mapID target="backIcon" url="icons/back.png" />\r
+   <mapID target="forwardIcon" url="icons/forward.png" />\r
+   <mapID target="homeIcon" url="icons/Home.png" />\r
+   <mapID target="printIcon" url="icons/print.png" />\r
+   <mapID target="printSetupIcon" url="icons/setup.png" />\r
+   \r
 </map>\r