Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / help / helpTOC.xml

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
deleted file mode 100755 (executable)
index 4338d36..0000000
--- a/help/helpTOC.xml
+++ /dev/null
@@ -1,99 +0,0 @@
-<?xml version="1.0" encoding="ISO-8859-1"  ?>
-<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
-<toc version="1.0">
-<tocitem text="Jalview Documentation" target="home" expand="true" >
-       <tocitem text="What's new" target="new" expand="true">
-      <tocitem text="Release History" target="release"/>
-         <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
-         <tocitem text="Mapping between Sequences" target="seqmappings"/>
-         <tocitem text="Coding Region Sequence Features" target="cdnafeatures"/>
-    </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="Sequence Features" target="seqfeatures" expand="false">
-          <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
-          <tocitem text="Sequence Features File" target="features.fileformat"/>
-          <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>
-       <tocitem text="Web Services" target="webservice" expand="false">
-          <tocitem text="Sequence Alignment" target="msaservice" expand="false">
-               <tocitem text="Clustal Alignment" target="clustal"/>
-                <tocitem text="Muscle Alignment" target="muscle"/>
-                <tocitem text="MAFFT Alignment" target="mafft"/>
-                <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
-            </tocitem>
-          <tocitem text="Secondary Structure Prediction" target="jnet"/>
-       </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="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="By Annotation" target="colours.annotation"/>
-       </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="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="Window Menus" target="menus" expand="false">
-               <tocitem text="Desktop Window" target="desktopMenu"/>
-               <tocitem text="Alignment Window" target="alMenu">
-                <tocitem text="File Menu" target="alwFile"/>
-                <tocitem text="Edit Menu" target="alwEdit"/>
-                               <tocitem text="Select Menu" target="alwSelect"/> 
-                <tocitem text="View Menu" target="alwView"/>
-                               <tocitem text="Format Menu" target="alwFormat"/>
-                <tocitem text="Colour Menu" target="alwColour"/>
-                <tocitem text="Calculation Menu" target="alwCalc"/>
-               <tocitem text="Web Service Menu" target="wsMenu"/>
-               <tocitem text="Annotation Menus" target="annotMenus"/>
-               <tocitem text="Popup Menu" target="popMenu"/>
-                </tocitem>
-       </tocitem>
-        <tocitem text="Preferences" target="preferences"/>
-       <tocitem text="Memory Settings" target="memory" expand="false">
-          <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
-          </tocitem>
-        <tocitem text="Command Line" target="commandline" expand="false">
-          <tocitem text="Command Line Arguments" target="clarguments"/>
-        </tocitem>
-</tocitem>
-<tocitem text="Useful information" expa nd="true">
-       <tocitem text="Amino Acid Table" target="aminoAcids"/>
-       <tocitem text="Amino Acid Properties" target="aaProperties"/>
-       <tocitem text="The Genetic Code" target="geneticCode"/>
-</tocitem>
-</toc>