-<tocitem text="Menus" expand="true" >\r
- <tocitem text="File" target="home"/>\r
- <tocitem text="Edit" target="home"/>\r
- <tocitem text="Font" target="home"/>\r
- <tocitem text="View" target="home"/>\r
- <tocitem text="Colour" target="colours">\r
+<tocitem text="Jalview Documentation" target="home" expand="true" >\r
+ <tocitem text="What's new" target="new" expand="false">\r
+ <tocitem text="Cursor Mode" target="cursor"/>\r
+ <tocitem text="Selection Area Based Editing" target="edit.selareas"/>\r
+ <tocitem text="User Defined Sequence Features" target="search"/>\r
+ <tocitem text="Sequence Feature Groups" target="seqfeatures"/>\r
+ <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
+ <tocitem text="Extended Sequence Feature Input File" target="features.fileformat"/>\r
+ <tocitem text="Annotations File" target="annotations.fileformat"/>\r
+ <tocitem text="Colour by Annotation Value" target="colours.annotation"/>\r
+ <tocitem text="Modeller PIR File IO" target="io.modellerpir"/>\r
+ </tocitem>\r
+ <tocitem text="Release History" target="release"/>\r
+ <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
+ <tocitem text="Conservation" target="calcs.alconserv"/>\r
+ <tocitem text="Quality" target="calcs.alquality"/>\r
+ <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
+ </tocitem>\r
+ <tocitem text="Input / Output" target="io"/>\r
+ <tocitem text="Key Strokes" target="keys"/>\r
+ <tocitem text="Making figures" target="export"/>\r
+ <tocitem text="Editing Alignments" target ="edit"/>\r
+ <tocitem text="Sequence Features" target="seqfeatures" expand="false">\r
+ <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
+ <tocitem text="Sequence Features File" target="features.fileformat"/>\r
+ </tocitem>\r
+ <tocitem text="Web Services" target="webservice" expand="false">\r
+ <tocitem text="Clustal Alignment" target="clustal"/>\r
+ <tocitem text="Muscle Alignment" target="muscle"/>\r
+ <tocitem text="JNet Prediction" target="jnet"/>\r
+ </tocitem>\r
+ <tocitem text="Colour Schemes" target="colours" expand="false">\r
+ <tocitem text="ClustalX" target="colours.clustal"/>\r