<?xml version="1.0" encoding="ISO-8859-1" ?>
-<!-- * 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)
- any later version. * * Jalview is distributed in the hope that it will be
- useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General
- Public License for more details. * * You should have received a copy of the
- GNU General Public License * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file. -->
-<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
+<!--
+ * 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) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<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="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="Select Columns by Annotation" target="selectcolbyannot" />
<tocitem text="Latest Release Notes" target="release"/>
</tocitem>
<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="Tree/PCA Input Data" target="recoverInputdata" />
<tocitem text="Pairwise Alignments" target="pairwise" />
<tocitem text="Remove Redundancy" target="redundancy" />
+ <tocitem text="Reference Sequences" target="referenceseq" />
</tocitem>
<tocitem text="Sequence Annotations" target="seqannots" expand="true">
<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="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" />