Merge branch 'develop' into bug/JAL-2225mapMultipleChains

[jalview.git] / src / jalview / gui / AnnotationColourChooser.java

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index f088791..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)
     {
-      oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
+      oldgroupColours = new Hashtable<>();
       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());
-    annotations = new JComboBox<String>(annotItems);
+    annotations = new JComboBox<>(annotItems);
 
     populateThresholdComboBox(threshold);
 
@@ -341,7 +341,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       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();
-    // 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)
   {
 
@@ -456,25 +453,10 @@ public class AnnotationColourChooser extends AnnotationRowFilter
         {
           continue;
         }
-
-        if (useOriginalColours.isSelected())
-        {
-          sg.setColourScheme(new AnnotationColourGradient(currentAnn,
-                  sg.getColourScheme(), selectedThresholdOption));
-          ((AnnotationColourGradient) sg.cs)
-                  .setSeqAssociated(seqAssociated.isSelected());
-        }
-        else
-        {
-          sg.setColourScheme(new AnnotationColourGradient(currentAnn,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  selectedThresholdOption));
-          ((AnnotationColourGradient) sg.cs)
-                  .setSeqAssociated(seqAssociated.isSelected());
-        }
+        sg.setColourScheme(
+                acg.getInstance(sg, ap.av.getHiddenRepSequences()));
       }
     }
-    return false;
   }
 
 }