JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index b547214..a48553e 100644 (file)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -283,9 +283,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter
   private void setDefaultMinMax()
   {
     minColour.setBackground(
-            Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+            Cache.getDefaultColour(Preferences.ANNOTATIONCOLOUR_MIN, Color.orange));
     maxColour.setBackground(
-            Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+            Cache.getDefaultColour(Preferences.ANNOTATIONCOLOUR_MAX, Color.red));
   }
 
   protected void showColourChooser(JPanel colourPanel, String titleKey)
@@ -301,14 +301,14 @@ public class AnnotationColourChooser extends AnnotationRowFilter
         updateView();
       }
     };
-    JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl,
+    JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), ttl,
             colourPanel.getBackground(), listener);
   }
 
   @Override
   public void reset()
   {
-    av.setGlobalColourScheme(oldcs);
+    this.ap.alignFrame.changeColour(oldcs);
     if (av.getAlignment().getGroups() != null)
     {
 
@@ -433,7 +433,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 
-    av.setGlobalColourScheme(acg);
+    this.ap.alignFrame.changeColour(acg);
 
     if (av.getAlignment().getGroups() != null)
     {
@@ -445,7 +445,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
           continue;
         }
         sg.setColourScheme(
-                acg.getInstance(sg, ap.av.getHiddenRepSequences()));
+                acg.getInstance(av, sg));
       }
     }
   }
@@ -456,5 +456,4 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     super.sliderDragReleased();
     ap.paintAlignment(true, true);
   }
-
 }