-<tocitem text="Jalview Documentation" target="home" expand="true" >
- <tocitem text="What's new" target="new" expand="true">
- <tocitem text="Protein Disorder Prediction" target="disorder"/>
- <tocitem text="Alignment Conservation Analysis" target="aacon"/>
- <tocitem text="Viewing RNA structure" target="varna" />
- <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
- <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
- <tocitem text="HTML annotation report" target="io.seqreport"/>
- <tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
- <tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
- <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
- <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
- <tocitem text="DNA or Protein PCA calculation" target="pca"/>
- <tocitem text="Normalised sequence logo display" target="calcs.consensus"/>
- </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="Multiple Views" target="multipleviews"/>
- <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
- <tocitem text="Fetching Sequences" target="seqfetch"/>
- <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
- <tocitem text="Viewing RNA structure" target="varna" />
- <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
- <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
- </tocitem>
- <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="Feature Colourschemes" target="features.featureschemes"/>
- <tocitem text="User Defined Sequence Features" target="seqfeatcreat"/>
- <tocitem text="Editing Sequence Features" target="seqfeatedit"/>
- <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
- <tocitem text="DAS Feature Settings" target="das.settings"/>
- <tocitem text="HTML annotation report" target="io.seqreport"/>
- </tocitem>
- <tocitem text="Web Services" target="webservice" expand="false">
- <tocitem text="JABAWS" target="jabaws"/>
- <tocitem text="Web Service Preferences" target="wsprefs"/>
- <tocitem text="Web Service Parameters" target="wsparams"/>
- <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="Protein Disorder Prediction" target="disorder"/>
- <tocitem text="Alignment Conservation Analysis" target="aacon"/>
- <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
- <tocitem text="Sequence Retrieval" target="seqfetch"/>
- <tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
- <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="ClustalX" target="colours.clustal"/>
- <tocitem text="Zappo" target="colours.zappo"/>
- <tocitem text="Taylor" target="colours.taylor"/>
- <tocitem text="Hydrophobicity" target="colours.hydro"/>
- <tocitem text="Helix propensity" target="colours.helix"/>
- <tocitem text="Strand propensity" target="colours.strand"/>
- <tocitem text="Turn propensity" target="colours.turn"/>
- <tocitem text="Buried index" target="colours.buried"/>
- <tocitem text="Nucleotide colours" target="colours.nucleotide"/>
- <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine"/>
- <tocitem text="Blosum62" target="colours.blosum"/>
- <tocitem text="by Percentage Identity" target="colours.pid"/>
- <tocitem text="User Defined" target="colours.user"/>
- <tocitem text="Above Percentage Identity" target="colours.abovepid"/>
- <tocitem text="By conservation" target="colours.conservation"/>
- <tocitem text="T-COFFEE Scores" target="io.tcoffeescores"/>
- <tocitem text="By Annotation" target="colours.annotation"/>
- <tocitem text="By RNA Helices" target="colours.rnahelices"/>
- </tocitem>
- <tocitem text="Calculations" target="calculations" expand="false">
- <tocitem text="Sorting alignments" target="sorting"/>
- <tocitem text="Calculating trees" target="trees"/>
- <tocitem text="Principal Component Analysis" target="pca"/>
- <tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
- <tocitem text="Pairwise Alignments" target="pairwise"/>
- <tocitem text="Remove Redundancy" target="redundancy"/>
- </tocitem>
- <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="RNA Structure Consensus" target="calcs.alstrconsensus"/>
- <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="Viewing RNA structures" target="varna" expand="false"> </tocitem>
- <tocitem text="VAMSAS Data Exchange" target="vamsas">
- <!-- what can Jalview share with other apps -->
- <!-- what other apps exist -->
+<!-- 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>
+
+ <tocitem text="Editing Alignments" target="edit" />
+ <tocitem text="Cursor Mode" target="cursor" />
+ <tocitem text="Key Strokes" target="keys" />
+
+ <tocitem text="Input / Output" target="io" expand="false">
+ <tocitem text="BioJSON v1.0" target="biojson" />
+ </tocitem>
+
+ <tocitem text="Making Figures" target="export" expand="false">
+ <tocitem text="BioJS MSA Viewer" target="biojsmsa" />
+ </tocitem>
+
+ <tocitem text="Hidden Regions" target="hiddenRegions" />
+ <tocitem text="Multiple Views" target="multipleviews" />
+ <tocitem text="Split Frame View" target="splitframe" />
+ <tocitem text="Viewing Trees" target="treeviewer" expand="false" />
+ <tocitem text="Fetching Sequences" target="seqfetch" />
+
+ <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="RNA Structure Consensus" target="calcs.alstrconsensus" />
+ <tocitem text="RNA Helices coloring" target="colours.rnahelices" />
+ </tocitem>
+
+ <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="Feature Colourschemes" target="features.featureschemes" />
+ <tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
+ <tocitem text="Editing Sequence Features" target="seqfeatedit" />
+ <tocitem text="DAS Feature Retrieval" target="das.viewing" />
+ <tocitem text="DAS Feature Settings" target="das.settings" />
+ <tocitem text="HTML annotation report" target="io.seqreport" />