Merge branch 'releases/Release_2_11_4_Branch'

[jalview.git] / help / help / helpTOC.xml

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 11f0541..259c43d 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -23,13 +23,10 @@
 <!-- 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">
 <!-- 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="Latest Release Notes" target="release"/>
-                       <tocitem text="Support for ChimeraX" target="chimera"/>
-                               <tocitem text="Support for Pymol" target="pymol"/>
-                               <tocitem text="Structures via 3D Beacons" target="structuresvia3dbeacons" />
-                               <tocitem text="Startup Memory Settings" target="startupprefs" />
-                       <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
-                       <tocitem text="Command line launch" target="jalviewcltool"/>
+                       <tocitem text="Latest Release Notes" target="release"/>
+                       <tocitem text="PaSiMap Sequence Similarity Plots" target="pasimap" />
+                       <tocitem text="Secondary Structure Trees and PCAs" target="proteinssanaly" />
+                       <tocitem text="Secondary Structure Consensus" target="proteinss" />                             

                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />

@@ -114,9 +111,10 @@
                
                <tocitem text="Calculations" expand="false">
                        <tocitem text="Sorting alignments" target="sorting" />
                
                <tocitem text="Calculations" expand="false">
                        <tocitem text="Sorting alignments" target="sorting" />

-                       <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+                       <tocitem text="Trees, PCA and PaSiMap" target="calcs.dialog" expand="false">

                          <tocitem text="Calculating trees" target="trees" />
                          <tocitem text="Principal Component Analysis" target="pca" />
                          <tocitem text="Calculating trees" target="trees" />
                          <tocitem text="Principal Component Analysis" target="pca" />

+                         <tocitem text="PaSiMap Analysis" target="pasimap" />

                        </tocitem>
                        <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
                        <tocitem text="Pairwise Alignments" target="pairwise" />
                        </tocitem>
                        <tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
                        <tocitem text="Pairwise Alignments" target="pairwise" />

@@ -169,12 +167,17 @@
                        <tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
                </tocitem>
                <tocitem text="Command Line" target="commandline" expand="false">
                        <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="Memory Settings" target="memory" expand="false"/>
-    <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>
-    </tocitem>
+                       <tocitem text="Command Line: introduction and reference" target="clarguments" />
+                       <tocitem text="Command Line: basic usage" target="clarguments-basic" />
+                       <tocitem text="Command Line: advanced usage" target="clarguments-advanced" />
+                       <tocitem text="Command Line: argument files" target="clarguments-argfiles" />
+                       <tocitem text="Command Line: reference" target="clarguments-reference" />
+                       <tocitem text="Command Line: old command line arguments" target="clarguments-old" />
+               </tocitem>
+               <tocitem text="Memory Settings" target="memory" expand="false"/>
+               <tocitem text="Jalview Launch Files" target="jvlfiles" expand="false"/>

                <tocitem text="Privacy" target="privacy" />
                <tocitem text="Privacy" target="privacy" />

-       </tocitem>
+    </tocitem>

        <tocitem text="Useful information" expand="true">
                <tocitem text="Amino Acid Table" target="aminoAcids" />
                <tocitem text="Amino Acid Properties" target="aaProperties" />
        <tocitem text="Useful information" expand="true">
                <tocitem text="Amino Acid Table" target="aminoAcids" />
                <tocitem text="Amino Acid Properties" target="aaProperties" />