JAL-1645 rejig bioJSON, export and whats new

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index b67eb6f..fe42110 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
-<!-- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) * 
-       Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. 
+<!-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * 
+       Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. 
        * * Jalview is free software: you can redistribute it and/or * modify it 
        under the terms of the GNU General Public License * as published by the Free 
        Software Foundation, either version 3 * of the License, or (at your option) 
@@ -14,28 +14,45 @@
 <toc version="1.0">
 <!-- 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="Annotation from Structure" target="xsspannotation" expand="false" />
-                       <tocitem text="Annotation Panel Menu" target="alwAnnotations" />
-                       <tocitem text="Add reference annotation" target="popMenuAddref" />
-                       <tocitem text="Colour By Annotation" target="colours.annotation" />
-                       <tocitem text="Chimera Viewer" target="chimera" />
-                       <tocitem text="Structure Preferences" target="strucprefs" />
+                       <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="Jmol Viewer" target="pdbjmol" />
+                               <tocitem text="Chimera Viewer" target="chimera" />
+                               <tocitem text="Select columns by annotation" target="selectcolbyannot" />
+                               <tocitem text="Annotations File Format" target="annotations.fileformat" />
+                               <tocitem text="BioJSON v1.0" target="biojson" />
+                               <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" />
-               <tocitem text="Making Figures" target="export" />
+               
+               <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="BioJSON v1.0" target="biojson" />
+                       <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="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" />
@@ -46,6 +63,7 @@
                        <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" />
@@ -62,6 +80,7 @@
                        <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" />
@@ -83,6 +102,7 @@
                        <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" />
@@ -91,17 +111,22 @@
                        <tocitem text="Pairwise Alignments" target="pairwise" />
                        <tocitem text="Remove Redundancy" target="redundancy" />
                </tocitem>
+               
                <tocitem text="Sequence Annotations" target="seqannots" expand="true">
                        <tocitem text="Annotation from Structure" target="xsspannotation" expand="false" />
                </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 text="Select Column by Annotation" target="calcs.annotation" />
                </tocitem>
-               <tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
+               <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" />