<!-- DO NOT WRAP THESE LINES - help2Website relies on each item being on one line! -->
<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
- <tocitem text="Split Frame View" target="splitframe" />
- <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
- <tocitem text="PDB Structure Chooser" target="pdbchooser" />
- <tocitem text="Chimera Viewer" target="chimera" />
- <tocitem text="Select columns by annotation" target="selectcolbyannot" />
<tocitem text="Latest Release Notes" target="release"/>
+ <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+ <tocitem text="Omit hidden regions in Overview" target="overview"/>
+ <tocitem text="identifers.org for URL Links" target="linksprefs" />
+ <tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
<tocitem text="Viewing Trees" target="treeviewer" expand="false" />
<tocitem text="Fetching Sequences" target="seqfetch" />
- <tocitem text="Select columns by annotation" target="selectcolbyannot" />
+ <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
<tocitem text="Viewing RNA structure" target="varna" />
<tocitem text="Sequence Alignment" target="msaservice" expand="false">
<tocitem text="Multiple Alignment Subjobs" target="msaservice" />
</tocitem>
- <tocitem text="Secondary Structure Prediction" target="jnet" />
+ <tocitem text="Secondary Structure Prediction" target="jpred" />
<tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold" />
<tocitem text="Protein Disorder Prediction" target="disorder" />
<tocitem text="Alignment Conservation Analysis" target="aacon" />
<tocitem text="By RNA Helices" target="colours.rnahelices" />
</tocitem>
- <tocitem text="Calculations" target="calculations" expand="false">
+ <tocitem text="Calculations" expand="false">
<tocitem text="Sorting alignments" target="sorting" />
<tocitem text="Calculating trees" target="trees" />
<tocitem text="Principal Component Analysis" target="pca" />
<tocitem text="Consensus" target="calcs.consensus" />
<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
<tocitem text="Annotations File Format" target="annotations.fileformat" />
- <tocitem text="Select Column by Annotation" target="calcs.annotation" />
+ <tocitem text="Select Columns by Annotation" target="selectcolbyannot" />
</tocitem>
<tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
<tocitem text="PDB Structure Chooser" target="pdbchooser" />
<tocitem text="Jmol Viewer" target="pdbjmol" />
- <tocitem text="Chimera Viewer" target="chimera" />
- <tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
+ <tocitem text="Chimera Viewer" target="chimera" />
</tocitem>
<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
+ <tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
+ <tocitem text="Configuring URL Links" target="linksprefs" />
+ </tocitem>
<tocitem text="VAMSAS Data Exchange" target="vamsas">
<!-- what can Jalview share with other apps -->
<!-- what other apps exist -->
<tocitem text="Annotations Menu" target="alwAnnotations" />
<tocitem text="Format Menu" target="alwFormat" />
<tocitem text="Colour Menu" target="alwColour" />
- <tocitem text="Calculation Menu" target="alwCalc" />
+ <tocitem text="Calculate Menu" target="alwCalc" />
<tocitem text="Web Service Menu" target="wsMenu" />
<tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
<tocitem text="Popup Menu" target="popMenu" />
</tocitem>
<tocitem text="Preferences" target="preferences" />
<tocitem text="Memory Settings" target="memory" expand="false"/>
+ <tocitem text="Scripting with Groovy" target="groovy">
+ <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+ </tocitem>
<tocitem text="Command Line" target="commandline" expand="false">
<tocitem text="Command Line Arguments" target="clarguments" />
- <tocitem text="Groovy Shell" target="groovy" />
</tocitem>
<tocitem text="Privacy" target="privacy" />
</tocitem>