X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2Fhelp.jhm;h=5fb79011a498d765c32506aa0d313b618f59fdfb;hb=HEAD;hp=449f34c3912b8228635f99af4d234fb1bdd78ce2;hpb=cc7e689bec78376ed404e42ec8f425496bb435c0;p=jalview.git

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 449f34c..f69547f 100755
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -60,9 +60,16 @@
    <mapID target="varna" url="html/features/varna.html"/>
    <mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
    <mapID target="preferences" url="html/features/preferences.html"/>     
+   <mapID target="startupprefs" url="html/features/preferences.html#startup"/>     
    <mapID target="strucprefs" url="html/features/preferences.html#structure"/>     
    <mapID target="commandline" url="html/features/commandline.html"/>
+   <mapID target="jalviewcltool" url="html/features/commandline.html#script"/>
    <mapID target="clarguments" url="html/features/clarguments.html"/>
+   <mapID target="clarguments-basic" url="html/features/clarguments-basic.html"/>
+   <mapID target="clarguments-advanced" url="html/features/clarguments-advanced.html"/>
+   <mapID target="clarguments-argfiles" url="html/features/clarguments-argfiles.html"/>
+   <mapID target="clarguments-reference" url="html/features/clarguments-reference.html"/>
+   <mapID target="clarguments-old" url="html/features/clarguments-old.html"/>
    <mapID target="jvlfiles" url="html/features/jvlfiles.html"/>
    <mapID target="io" url="html/io/index.html"/>
    <mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
@@ -82,6 +89,9 @@
    <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="pasimap" url="html/calculations/pasimap.html"/>
+   <mapID target="proteinss" url="html/calculations/protssconsensus.html"/>
+   <mapID target="proteinssanaly" url="html/calculations/tree.html#ssim"/>
    <mapID target="pca" url="html/calculations/pca.html"/>
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>
    <mapID target="redundancy" url="html/calculations/redundancy.html"/>
@@ -93,12 +103,17 @@
    <mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>
    <mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />
    <mapID target="colours.taylor" url="html/colourSchemes/taylor.html" />
+   <mapID target="colours.gecos-flower" url="html/colourSchemes/gecos-flower.html" />
+   <mapID target="colours.gecos-blossom" url="html/colourSchemes/gecos-blossom.html" />
+   <mapID target="colours.gecos-sunset" url="html/colourSchemes/gecos-sunset.html" />
+   <mapID target="colours.gecos-ocean" url="html/colourSchemes/gecos-ocean.html" />
    <mapID target="colours.hydro" url="html/colourSchemes/hydrophobic.html" />
    <mapID target="colours.helix" url="html/colourSchemes/helix.html" />
    <mapID target="colours.strand" url="html/colourSchemes/strand.html" />
    <mapID target="colours.turn" url="html/colourSchemes/turn.html" />
    <mapID target="colours.buried" url="html/colourSchemes/buried.html" />
    <mapID target="colours.nucleotide" url="html/colourSchemes/nucleotide.html" />
+   <mapID target="colours.nucleotideambiguity" url="html/colourSchemes/nucleotideambiguity.html" />
    <mapID target="colours.blosum" url="html/colourSchemes/blosum.html" />
    <mapID target="colours.pid" url="html/colourSchemes/pid.html" />
    <mapID target="colours.user" url="html/colourSchemes/user.html"/>
@@ -149,6 +164,10 @@
    <mapID target="pdbfts" url="html/features/pdbsequencefetcher.html#pdbfts" />
    <mapID target="siftsmapping" url="html/features/siftsmapping.html" />
    <mapID target="pdbchooser" url="html/features/structurechooser.html" />
+   <mapID target="structureandpaefromfile" url="html/features/structurechooser.html#loadfromfile" />
+   <mapID target="structuresvia3dbeacons" url="html/features/structurechooser.html#3dbeaconssearch" />   
+   <mapID target="workingwithpae" url="html/features/paematrices.html" />
+   <mapID target="paematrixformat" url="html/io/paematrixformat.html" />
    <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
    <mapID target="biojsmsa" url="html/features/biojsmsa.html" />