Merge remote-tracking branch 'origin/develop' into

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index e2d986e..2fc5716 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -248,6 +249,7 @@ public class OverviewPanel extends Panel implements Runnable,
     int sameCol = 0;
 
     SequenceI seq = null;
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
 
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
@@ -277,7 +279,7 @@ public class OverviewPanel extends Panel implements Runnable,
             lastcol = (int) (col * sampleCol);
 
             color = getColumnColourFromSequence(seq, hiddenRow,
-                    hasHiddenCols, lastcol);
+                    hasHiddenCols, lastcol, finder);
 
             mg.setColor(color);
             if (sameCol == 1 && sameRow == 1)
@@ -305,21 +307,12 @@ public class OverviewPanel extends Panel implements Runnable,
    */
   private Color getColumnColourFromSequence(
           jalview.datamodel.SequenceI seq, boolean hiddenRow,
-          boolean hasHiddenCols, int lastcol)
+          boolean hasHiddenCols, int lastcol, FeatureColourFinder finder)
   {
-    Color color;
+    Color color = Color.white;
     if (seq.getLength() > lastcol)
     {
-      color = sr.getResidueBoxColour(seq, lastcol);
-
-      if (av.isShowSequenceFeatures())
-      {
-        color = fr.findFeatureColour(color, seq, lastcol);
-      }
-    }
-    else
-    {
-      color = Color.white;
+      color = sr.getResidueColour(seq, lastcol, finder);
     }
 
     if (hiddenRow