X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhelp.jhm;h=5fb79011a498d765c32506aa0d313b618f59fdfb;hb=958a0e91dec242191ec7543ab3f23b7e508e1112;hp=6b06d36f7e54098eda6c7d51ddcde68e4afe8266;hpb=a7818bc128f2dd28fbbde47b938266691fac1063;p=jalview.git

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 6b06d36..5fb7901 100755
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -65,6 +65,11 @@
    <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"/>
@@ -95,12 +100,17 @@
    <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"/>
@@ -151,7 +161,10 @@
    <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" />