Merge branch 'develop' into bug/JAL-2346annotationChoice

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

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index d4a21b2..f516bc9 100644 (file)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -20,6 +20,12 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
 import java.awt.BorderLayout;
 import java.awt.Button;
 import java.awt.Checkbox;
@@ -44,12 +50,6 @@ import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
 public class AnnotationColourChooser extends Panel implements
         ActionListener, AdjustmentListener, ItemListener, MouseListener
 {
@@ -88,10 +88,7 @@ public class AnnotationColourChooser extends Panel implements
       oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        if (sg.cs != null)
-        {
-          oldgroupColours.put(sg, sg.cs);
-        }
+        oldgroupColours.put(sg, sg.getColourScheme());
       }
     }
     this.av = av;
@@ -519,8 +516,6 @@ public class AnnotationColourChooser extends Panel implements
     AnnotationColourGradient acg = null;
     if (currentColours.getState())
     {
-      acg = new AnnotationColourGradient(currentAnnotation,
-              av.getGlobalColourScheme(), aboveThreshold);
     }
     else
     {
@@ -544,21 +539,21 @@ public class AnnotationColourChooser extends Panel implements
     {
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        if (sg.cs == null)
+        if (sg.getColourScheme() == null)
         {
           continue;
         }
 
         if (currentColours.getState())
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
-                  aboveThreshold);
+          sg.setColourScheme(new AnnotationColourGradient(
+                  currentAnnotation, sg.getColourScheme(), aboveThreshold));
         }
         else
         {
-          sg.cs = new AnnotationColourGradient(currentAnnotation,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  aboveThreshold);
+          sg.setColourScheme(new AnnotationColourGradient(
+                  currentAnnotation, minColour.getBackground(), maxColour
+                          .getBackground(), aboveThreshold));
         }
       }
     }
@@ -575,11 +570,10 @@ public class AnnotationColourChooser extends Panel implements
     {
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        sg.cs = oldgroupColours.get(sg);
+        sg.setColourScheme(oldgroupColours.get(sg));
       }
     }
     ap.paintAlignment(true);
-
   }
 
   @Override