<toc version="1.0">\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 text="MAFFT Alignment" target="mafft"/>\r
+ <tocitem text="DAS Feature Fetching" target="das.settings"/>\r
+ <tocitem text="Hide Regions" target="hiddenRegions"/> \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="Consensus" target="calcs.consensus"/>\r
- <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
- </tocitem>\r
- <tocitem text="Input / Output" target="io"/>\r
+ <tocitem text="Release History" target="release"/>\r
+ <tocitem text="Editing Alignments" target ="edit"/> \r
+ <tocitem text="Cursor Mode" target="cursor"/>\r
<tocitem text="Key Strokes" target="keys"/>\r
+ <tocitem text="Input / Output" target="io"/>\r
<tocitem text="Making figures" target="export"/>\r
- <tocitem text="Editing Alignments" target ="edit"/>\r
+ <tocitem text="Hidden Regions" target="hiddenRegions"/>\r
+ <tocitem text="Viewing PDB Files" target="viewingpdbs"/>\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 text="User Defined Sequence Features" target="search"/>\r
+ <tocitem text="DAS Features Settings" target="das.settings"/>\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="MAFFT Alignment" target="mafft"/>\r
<tocitem text="JNet Prediction" target="jnet"/>\r
</tocitem>\r
<tocitem text="Colour Schemes" target="colours" expand="false">\r
<tocitem text="Pairwise Alignments" target="pairwise"/>\r
<tocitem text="Remove Redundancy" target="redundancy"/>\r
</tocitem>\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="Consensus" target="calcs.consensus"/>\r
+ <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
+ </tocitem>\r
<tocitem text="Window Menus" target="menus" expand="false">\r
<tocitem text="Desktop Window" target="desktopMenu"/>\r
<tocitem text="Alignment Window" target="alMenu">\r