X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp.jhm;h=261d6d0c5847119fd98de5c3ddfdcc368499b291;hb=0e1692ebb479ee94f412079c50be4e0222bd1776;hp=176569b6bfd2d42c916327213a314c33062983af;hpb=96b6991703b70a1bbb0491f9946d397c9fcf5a38;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index 176569b..261d6d0 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -11,31 +11,41 @@
    <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="jabaws" url="html/webServices/JABAWS.html"/>
+   <mapID target="wsparams" url="html/webServices/webServicesParams.html"/>
+   <mapID target="wsprefs" url="html/webServices/webServicesPrefs.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="shmrws" url="html/webServices/shmr.html"/>
+   <mapID target="newsreader" url="html/webServices/newsreader.html"/>
    <mapID target="seqfetch" url="html/features/seqfetch.html"/>
+   <mapID target="dbreffetcher" url="html/webservices/dbreffetcher.html"/>
+   <mapID target="seqmappings" url="html/features/seqmappings.html"/>
+   <mapID target="cdnafeatures" url="html/features/codingfeatures.html"/>
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
    <mapID target="seqfeatedit" url="html/features/editingFeatures.html"/>
    <mapID target="seqfeatcreat" url="html/features/creatinFeatures.html"/>
    <mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
+   <mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
+   <mapID target="pdbjmol" url="html/features/jmol.html"/>
    <mapID target="preferences" url="html/features/preferences.html"/>     
+   <mapID target="commandline" url="html/features/commandline.html"/>
+   <mapID target="clarguments" url="html/features/clarguments.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="features.featureschemes" url="html/features/featureschemes.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="multipleviews" url="html/features/multipleViews.html"/>
-   <mapID target="reloadsave" url="html/features/reloadSave.html"/>
    <mapID target="trees" url="html/calculations/tree.html"/>
+   <mapID target="treeviewer" url="html/calculations/treeviewer.html"/>
    <mapID target="sorting" url="html/calculations/sorting.html"/>
    <mapID target="pca" url="html/calculations/pca.html"/>
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>
@@ -81,7 +91,9 @@
    
    <mapID target="memory" url="html/memory.html" />
    <mapID target="jalviewjnlp" url="html/jalviewjnlp.html" />
-   
+   <mapID target="groovy" url="html/features/groovy.html" />
+   <mapID target="privacy" url="html/privacy.html" />
+   <mapID target="vamsas" url="html/vamsas/index.html"/>
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
    <mapID target="aaProperties" url="html/misc/aaproperties.html" />
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />