JAL-2094 first pass with jalview.api.ColorI interface

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 1749e23..edf8645 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.datamodel.AlignmentI;
+import jalview.util.ColorUtils;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -298,6 +299,8 @@ public class OverviewPanel extends Panel implements Runnable,
     Color color = Color.yellow;
     int row, col, sameRow = 0, sameCol = 0;
     jalview.datamodel.SequenceI seq;
+    final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+            .hasHiddenColumns();
     boolean hiddenRow = false;
     AlignmentI alignment = av.getAlignment();
     for (row = 0; row <= sequencesHeight; row++)
@@ -309,7 +312,7 @@ public class OverviewPanel extends Panel implements Runnable,
       }
 
       hiddenRow = false;
-      if (av.hasHiddenRows())
+      if (hasHiddenRows)
       {
         seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
         if (seq == null)
@@ -342,11 +345,12 @@ public class OverviewPanel extends Panel implements Runnable,
 
         if (seq.getLength() > lastcol)
         {
-          color = sr.getResidueBoxColour(seq, lastcol);
+          color = ColorUtils.getColor(sr.getResidueBoxColour(seq, lastcol));
 
           if (av.isShowSequenceFeatures())
           {
-            color = fr.findFeatureColour(color, seq, lastcol);
+            color = ColorUtils.getColor(fr.findFeatureColour(color, seq,
+                    lastcol));
           }
         }
         else
@@ -355,8 +359,8 @@ public class OverviewPanel extends Panel implements Runnable,
         }
 
         if (hiddenRow
-                || (av.hasHiddenColumns() && !av.getColumnSelection()
-                        .isVisible(lastcol)))
+                || (hasHiddenCols && !av.getColumnSelection().isVisible(
+                        lastcol)))
         {
           color = color.darker().darker();
         }