X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhelp%2Fhelp.jhm;h=6b06d36f7e54098eda6c7d51ddcde68e4afe8266;hb=dceb54d45477a8af0632b703c53254c9a80a11db;hp=64f3d2178b2b5da9bf48e05f17c84081db5a6e3c;hpb=7bb2a1c049e7b7be9c04012ce90afc173b81eb1a;p=jalview.git

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 64f3d21..6b06d36 100755
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -47,6 +47,7 @@
    <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.report" url="html/features/seqfeaturereport.html"/>
    <mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
    <mapID target="seqfeatures.settings.selcols" url="html/features/featuresettings.html#selectbyfeature"/>
    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
@@ -54,13 +55,17 @@
    <mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
    <mapID target="pdbjmol" url="html/features/jmol.html"/>
    <mapID target="chimera" url="html/features/chimera.html"/>
+   <mapID target="pymol" url="html/features/pymol.html"/>
    <mapID target="chimera.annotxfer" url="html/features/chimera.html#annotxfer"/>
    <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="jvlfiles" url="html/features/jvlfiles.html"/>
    <mapID target="io" url="html/io/index.html"/>
    <mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
    <mapID target="io.seqreport" url="html/io/exportseqreport.html"/>
@@ -74,6 +79,7 @@
    <mapID target="jalarchive" url="html/features/jalarchive.html"/>
    <mapID target="multipleviews" url="html/features/multipleViews.html"/>
    <mapID target="splitframe" url="html/features/splitView.html"/>
+   <mapID target="splitframe.virtualfeats" url="html/features/splitView.html#virtualfeats"/>
    <mapID target="splitframe.mirrorfonts" url="html/features/splitView.html#mirror"/>
    <mapID target="trees" url="html/calculations/tree.html"/>
    <mapID target="treeviewer" url="html/calculations/treeviewer.html"/>
@@ -134,7 +140,6 @@
    <mapID target="groovy.colours" url="html/features/groovy.html#groovyColours" />
    <mapID target="groovy.featurescounter" url="html/groovy/featuresCounter.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" />
@@ -146,6 +151,7 @@
    <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="structuresvia3dbeacons" url="html/features/structurechooser.html#3dbeaconssearch" />   
    <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
    <mapID target="biojsmsa" url="html/features/biojsmsa.html" />
    
@@ -167,4 +173,6 @@
    <mapID target="overviewprefs" url="html/features/preferences.html#overview" />
    
    <mapID target="importvcf" url="html/features/importvcf.html" />
+   <mapID target="importvcf.attribs" url="html/features/importvcf.html#attribs" />
+   <mapID target="logging" url="html/logging.html" />
 </map>