<tocitem text="Jalview Documentation" target="home" expand="true" >
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Release History" target="release"/>
- <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
- <tocitem text="Mapping between Sequences" target="seqmappings"/>
- </tocitem>
+ <tocitem text="Sequence Retrieval" target="seqfetch"/>
+ <tocitem text="VAMSAS Interoperation" target="vamsas"/>
+ </tocitem>
<tocitem text="Editing Alignments" target ="edit"/>
<tocitem text="Cursor Mode" target="cursor"/>
<tocitem text="Key Strokes" target="keys"/>
<tocitem text="Input / Output" target="io"/>
- <tocitem text="Making figures" target="export"/>
+ <tocitem text="Making Figures" target="export"/>
<tocitem text="Hidden Regions" target="hiddenRegions"/>
<tocitem text="Multiple Views" target="multipleviews"/>
+ <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
+ <tocitem text="Fetching Sequences" target="seqfetch"/>
<tocitem text="Sequence Features" target="seqfeatures" expand="false">
<tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
<tocitem text="Sequence Features File" target="features.fileformat"/>
<tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
</tocitem>
<tocitem text="Secondary Structure Prediction" target="jnet"/>
+ <tocitem text="Sequence Retrieval" target="seqfetch"/>
+ <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
</tocitem>
<tocitem text="Colour Schemes" target="colours" expand="false">
<tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
<tocitem text="Pairwise Alignments" target="pairwise"/>
<tocitem text="Remove Redundancy" target="redundancy"/>
</tocitem>
- <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
+ <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
<tocitem text="Conservation" target="calcs.alconserv"/>
<tocitem text="Quality" target="calcs.alquality"/>
<tocitem text="Consensus" target="calcs.consensus"/>
<tocitem text="Jmol Viewer" target="pdbjmol"/>
<tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
</tocitem>
+ <tocitem text="VAMSAS Data Exchange" target="vamsas">
+ <!-- what can Jalview share with other apps -->
+ <!-- what other apps exist -->
+ </tocitem>
<tocitem text="Window Menus" target="menus" expand="false">
<tocitem text="Desktop Window" target="desktopMenu"/>
<tocitem text="Alignment Window" target="alMenu">
</tocitem>
<tocitem text="Command Line" target="commandline" expand="false">
<tocitem text="Command Line Arguments" target="clarguments"/>
+ <tocitem text="Groovy Shell" target="groovy"/>
</tocitem>
</tocitem>
<tocitem text="Useful information" expa nd="true">