Merge branch 'develop' into features/JAL-2909_bamImport2_11

diff --git a/src/jalview/gui/AquaInternalFrameManager.java b/src/jalview/gui/AquaInternalFrameManager.java
index 829135b..537ec17 100644 (file)
--- a/src/jalview/gui/AquaInternalFrameManager.java
+++ b/src/jalview/gui/AquaInternalFrameManager.java
@@ -60,6 +60,7 @@ import javax.swing.JInternalFrame;
  * around to the bottom of the window stack (as the original implementation
  * does)
  * 
+ * see com.sun.java.swing.plaf.windows.WindowsDesktopManager
  */
 public class AquaInternalFrameManager extends DefaultDesktopManager
 {
@@ -253,4 +254,4 @@ public class AquaInternalFrameManager extends DefaultDesktopManager
   {
     switchFrame(false);
   }
-}
\ No newline at end of file
+}

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index 1c50aab..f36461a 100644 (file)
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -230,13 +230,12 @@ public class OverviewRenderer
           jalview.datamodel.SequenceI seq,
           int lastcol, FeatureColourFinder fcfinder)
   {
-    Color color = Color.white;
+    Color color = resColFinder.GAP_COLOUR;
 
     if ((seq != null) && (seq.getLength() > lastcol))
     {
       color = resColFinder.getResidueColour(true, shader, allGroups, seq,
-              lastcol,
-              fcfinder);
+              lastcol, fcfinder);
     }
 
     return color.getRGB();

diff --git a/test/jalview/gui/SeqCanvasTest.java b/test/jalview/gui/SeqCanvasTest.java
index 05b9aea..51fa5ce 100644 (file)
--- a/test/jalview/gui/SeqCanvasTest.java
+++ b/test/jalview/gui/SeqCanvasTest.java
@@ -9,8 +9,6 @@ import jalview.io.FileLoader;
 import java.awt.Font;
 import java.awt.FontMetrics;
 
-import junit.extensions.PA;
-
 import org.testng.annotations.Test;
 
 public class SeqCanvasTest