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JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationColourChooser.java
diff --git
a/src/jalview/gui/AnnotationColourChooser.java
b/src/jalview/gui/AnnotationColourChooser.java
index
8d123bb
..
153f70c
100644
(file)
--- a/
src/jalview/gui/AnnotationColourChooser.java
+++ b/
src/jalview/gui/AnnotationColourChooser.java
@@
-79,7
+79,7
@@
public class AnnotationColourChooser extends AnnotationRowFilter
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.av.getAlignment().getGroups())
{
if (sg.getColourScheme() != null)
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
if (sg.getColourScheme() != null)
@@
-122,7
+122,7
@@
public class AnnotationColourChooser extends AnnotationRowFilter
}
Vector<String> annotItems = getAnnotationItems(
seqAssociated.isSelected());
}
Vector<String> annotItems = getAnnotationItems(
seqAssociated.isSelected());
- annotations = new JComboBox<String>(annotItems);
+ annotations = new JComboBox<>(annotItems);
populateThresholdComboBox(threshold);
populateThresholdComboBox(threshold);
@@
-341,7
+341,7
@@
public class AnnotationColourChooser extends AnnotationRowFilter
getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
propagateSeqAssociatedThreshold(updateAllAnnotation,
getCurrentAnnotation());
getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
propagateSeqAssociatedThreshold(updateAllAnnotation,
getCurrentAnnotation());
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
}
}
@@
-415,12
+415,9
@@
public class AnnotationColourChooser extends AnnotationRowFilter
colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
ap.alignmentChanged();
colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
ap.alignmentChanged();
- // ensure all associated views (overviews, structures, etc) are notified of
- // updated colours.
- ap.paintAlignment(true);
}
}
- protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn,
+ protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
int selectedThresholdOption)
{
int selectedThresholdOption)
{
@@
-460,7
+457,6
@@
public class AnnotationColourChooser extends AnnotationRowFilter
acg.getInstance(sg, ap.av.getHiddenRepSequences()));
}
}
acg.getInstance(sg, ap.av.getHiddenRepSequences()));
}
}
- return false;
}
}
}
}