X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=6eca05ed752a4be98ab11e3025a92cf426891bd9;hb=da1ce6ca071deb35b983a41f6eeed43f30b3c3b2;hp=8de751a74c264438a823d3d2e29fb478316a418c;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 8de751a..6eca05e 100644
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -22,6 +22,7 @@ package jalview.appletgui;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
+import jalview.gui.Preferences;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
@@ -85,7 +86,7 @@ public class AnnotationColourChooser extends Panel implements
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
-      oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
+      oldgroupColours = new HashMap<>();
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
         oldgroupColours.put(sg, sg.getColourScheme());
@@ -180,8 +181,8 @@ public class AnnotationColourChooser extends Panel implements
     // TODO remove duplication with gui.AnnotationRowFilter
     // TODO add 'per sequence only' option / parameter
 
-    annotationLabels = new HashMap<AlignmentAnnotation, String>();
-    Vector<String> list = new Vector<String>();
+    annotationLabels = new HashMap<>();
+    Vector<String> list = new Vector<>();
     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
     if (anns == null)
     {
@@ -217,9 +218,9 @@ public class AnnotationColourChooser extends Panel implements
   private void setDefaultMinMax()
   {
     minColour.setBackground(av.applet.getDefaultColourParameter(
-            "ANNOTATIONCOLOUR_MIN", Color.orange));
+            Preferences.ANNOTATIONCOLOUR_MIN, Color.orange));
     maxColour.setBackground(av.applet
-            .getDefaultColourParameter("ANNOTATIONCOLOUR_MAX", Color.red));
+            .getDefaultColourParameter(Preferences.ANNOTATIONCOLOUR_MAX, Color.red));
 
   }
 
@@ -376,7 +377,7 @@ public class AnnotationColourChooser extends Panel implements
     else if (evt.getSource() == cancel)
     {
       reset();
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
       frame.setVisible(false);
     }
 
@@ -417,7 +418,7 @@ public class AnnotationColourChooser extends Panel implements
       }
 
       currentAnnotation.threshold.value = slider.getValue() / 1000f;
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -559,7 +560,7 @@ public class AnnotationColourChooser extends Panel implements
 
     // update colours in linked windows
     ap.alignmentChanged();
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   void reset()
@@ -572,7 +573,7 @@ public class AnnotationColourChooser extends Panel implements
         sg.setColourScheme(oldgroupColours.get(sg));
       }
     }
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   @Override
@@ -588,7 +589,7 @@ public class AnnotationColourChooser extends Panel implements
   @Override
   public void mouseReleased(MouseEvent evt)
   {
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   @Override