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Merge branch 'documentation/JAL-2698_release2103' into develop
[jalview.git]
/
help
/
helpTOC.xml
diff --git
a/help/helpTOC.xml
b/help/helpTOC.xml
index
db47351
..
4636ea3
100755
(executable)
--- a/
help/helpTOC.xml
+++ b/
help/helpTOC.xml
@@
-24,9
+24,13
@@
<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="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Latest Release Notes" target="release"/>
+ <tocitem text="Calculations Dialog" target="calcs.dialog"/>
<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+ <tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
<tocitem text="Omit hidden regions in Overview" target="overview"/>
<tocitem text="Omit hidden regions in Overview" target="overview"/>
- <tocitem text="Split Frame View" target="splitframe.mirrorfonts" />
+ <tocitem text="Show gaps as grey in overview" target="overviewprefs"/>
+ <tocitem text="identifers.org for URL Links" target="linksprefs" />
+ <tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
@@
-107,8
+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="Calculating trees" target="trees" />
- <tocitem text="Principal Component Analysis" target="pca" />
+ <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+ <tocitem text="Calculating trees" target="trees" />
+ <tocitem text="Principal Component Analysis" target="pca" />
+ </tocitem>
<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
<tocitem text="Pairwise Alignments" target="pairwise" />
<tocitem text="Remove Redundancy" target="redundancy" />
<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
<tocitem text="Pairwise Alignments" target="pairwise" />
<tocitem text="Remove Redundancy" target="redundancy" />
@@
-135,7
+141,7
@@
</tocitem>
<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
</tocitem>
<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
- <tocitem text="Configuring URL Links" target="linkspref" />
+ <tocitem text="Configuring URL Links" target="linksprefs" />
</tocitem>
<tocitem text="VAMSAS Data Exchange" target="vamsas">
<!-- what can Jalview share with other apps -->
</tocitem>
<tocitem text="VAMSAS Data Exchange" target="vamsas">
<!-- what can Jalview share with other apps -->