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JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...
[jalview.git]
/
src
/
jalview
/
schemes
/
RNAHelicesColourChooser.java
diff --git
a/src/jalview/schemes/RNAHelicesColourChooser.java
b/src/jalview/schemes/RNAHelicesColourChooser.java
index
90cc14f
..
9809fa9
100644
(file)
--- a/
src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/
src/jalview/schemes/RNAHelicesColourChooser.java
@@
-58,12
+58,12
@@
public class RNAHelicesColourChooser
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
+ oldgroupColours = new Hashtable<>();
for (SequenceGroup sg : ap.getAlignment().getGroups())
{
for (SequenceGroup sg : ap.getAlignment().getGroups())
{
- if (sg.cs != null)
+ if (sg.getColourScheme() != null)
{
{
- oldgroupColours.put(sg, sg.cs);
+ oldgroupColours.put(sg, sg.getColourScheme());
}
}
}
}
}
}
@@
-71,7
+71,7
@@
public class RNAHelicesColourChooser
this.ap = ap;
adjusting = true;
this.ap = ap;
adjusting = true;
- Vector<String> list = new Vector<String>();
+ Vector<String> list = new Vector<>();
int index = 1;
AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
if (anns != null)
int index = 1;
AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
if (anns != null)
@@
-105,6
+105,6
@@
public class RNAHelicesColourChooser
av.setGlobalColourScheme(rhc);
av.setGlobalColourScheme(rhc);
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
}
}
}