From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 17 Oct 2013 11:33:32 +0000 (+0100)
Subject: fix for JAL-1398 - original colourscheme is enabled if colourscheme has a BaseColour... 
X-Git-Tag: Jalview_2_9~218^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c9fd7ec6f8096c6659cccfc0aad0c2d5fd9ed9d1;hp=3b4eda86f1f240a932cc778658dc1fbe56e9630d;p=jalview.git

fix for JAL-1398 - original colourscheme is enabled if colourscheme has a BaseColour setting.
See JAL-1399 for future improvements.
---

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index f9594eb..3c0f704 100644
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -81,18 +81,19 @@ public class AnnotationColourChooser extends Panel implements
 
     setDefaultMinMax();
 
+    adjusting = true;
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setState(acg.isPredefinedColours());
-      if (!acg.isPredefinedColours())
+      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;
@@ -492,6 +493,7 @@ public class AnnotationColourChooser extends Panel implements
     }
 
     // update colours in linked windows
+    ap.alignmentChanged();
     ap.paintAlignment(true);
   }
 
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 3278a76..5ee69f2 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -120,18 +120,19 @@ public class AnnotationColourChooser extends JPanel
     // Always get default shading from preferences.
     setDefaultMinMax();
 
+    adjusting = true;
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setSelected(acg.isPredefinedColours());
-      if (!acg.isPredefinedColours())
+      currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
+      if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
       {
         minColour.setBackground(acg.getMinColour());
         maxColour.setBackground(acg.getMaxColour());
       }
       seqAssociated.setSelected(acg.isSeqAssociated());
+      
     }
-    adjusting = true;
     annotations = new JComboBox(
             getAnnotationItems(seqAssociated.isSelected()));