Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge

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

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 5f61ead..27d5497 100644 (file)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
@@ -81,18 +82,19 @@ public class AnnotationColourChooser extends Panel implements
 
     setDefaultMinMax();
 
+    adjusting = true;
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setState(acg.predefinedColours);
-      if (!acg.predefinedColours)
+      currentColours.setState(acg.isPredefinedColours() || acg.getBaseColour()!=null);
+      if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
       {
         minColour.setBackground(acg.getMinColour());
         maxColour.setBackground(acg.getMaxColour());
       }
+      // seqAssociated.setState(acg.isSeqAssociated());
     }
 
-    adjusting = true;
 
     Vector list = new Vector();
     int index = 1;
@@ -458,13 +460,14 @@ public class AnnotationColourChooser extends Panel implements
     if (currentAnnotation.graphMin == 0f
             && currentAnnotation.graphMax == 0f)
     {
-      acg.predefinedColours = true;
+      acg.setPredefinedColours(true);
     }
 
     acg.thresholdIsMinMax = thresholdIsMin.getState();
 
     av.setGlobalColourScheme(acg);
 
+    // TODO: per group colour propagation not always desired
     if (av.getAlignment().getGroups() != null)
     {
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
@@ -491,6 +494,7 @@ public class AnnotationColourChooser extends Panel implements
     }
 
     // update colours in linked windows
+    ap.alignmentChanged();
     ap.paintAlignment(true);
   }