<toc version="1.0">
<tocitem text="Jalview Documentation" target="home" expand="true" >
<tocitem text="What's new" target="new" expand="true">
- <tocitem text="Multiple Views" target="multipleviews"/>
- <tocitem text="New keystrokes and Menus" target="newkeys"/>
- <tocitem text="Reload and Save" target="reloadsave"/>
- <tocitem text="Creating Sequence Features" target="seqfeatcreat"/>
- <tocitem text="Amending or Deleting Sequence Features" target="seqfeatedit"/>
- <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
- </tocitem>
- <tocitem text="Release History" target="release"/>
- <tocitem text="Editing Alignments" target ="edit"/>
- <tocitem text="Cursor Mode" target="cursor"/>
+ <tocitem text="Release History" target="release"/>
+ <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
+ <tocitem text="Mapping between Sequences" target="seqmappings"/>
+ </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="Hidden Regions" target="hiddenRegions"/>
- <tocitem text="Viewing PDB Files" target="viewingpdbs"/>
+ <tocitem text="Multiple Views" target="multipleviews"/>
<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="Secondary Structure Prediction" target="jnet"/>
</tocitem>
<tocitem text="Colour Schemes" target="colours" expand="false">
+ <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
<tocitem text="ClustalX" target="colours.clustal"/>
<tocitem text="Zappo" target="colours.zappo"/>
<tocitem text="Taylor" target="colours.taylor"/>
<tocitem text="Consensus" target="calcs.consensus"/>
<tocitem text="Annotations File Format" target="annotations.fileformat"/>
</tocitem>
+ <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
+ <tocitem text="Jmol Viewer" target="pdbjmol"/>
+ <tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
+ </tocitem>
<tocitem text="Window Menus" target="menus" expand="false">
<tocitem text="Desktop Window" target="desktopMenu"/>
<tocitem text="Alignment Window" target="alMenu">
<tocitem text="Popup Menu" target="popMenu"/>
</tocitem>
</tocitem>
+ <tocitem text="Preferences" target="preferences"/>
<tocitem text="Memory Settings" target="memory" expand="false">
<tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
</tocitem>
+ <tocitem text="Command Line" target="commandline" expand="false">
+ <tocitem text="Command Line Arguments" target="clarguments"/>
+ </tocitem>
</tocitem>
-<tocitem text="Useful information" expand="true">
+<tocitem text="Useful information" expa nd="true">
<tocitem text="Amino Acid Table" target="aminoAcids"/>
<tocitem text="Amino Acid Properties" target="aaProperties"/>
<tocitem text="The Genetic Code" target="geneticCode"/>