Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index ac2138f..19158fd 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -90,7 +90,9 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.forOverview = true;
     fr = new FeatureRenderer(ap);
 
-    od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
+    od = new OverviewDimensions(av.getRanges(),
+            (av.isShowAnnotation() && av
+                    .getAlignmentConservationAnnotation() != null));
 
     addComponentListener(new ComponentAdapter()
     {
@@ -199,9 +201,12 @@ public class OverviewPanel extends JPanel implements Runnable
     float sampleCol = alwidth / (float) od.getWidth();
     float sampleRow = alheight / (float) od.getSequencesHeight();
 
+    long start = System.currentTimeMillis();
     buildImage(sampleRow, sampleCol);
 
-    if (av.isShowAnnotation())
+    // check for conservation annotation to make sure overview works for DNA too
+    if (av.isShowAnnotation()
+            && (av.getAlignmentConservationAnnotation() != null))
     {
       renderer.updateFromAlignViewport(av);
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
@@ -215,6 +220,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
       }
     }
+    System.out.println("Overview took "
+            + (System.currentTimeMillis() - start) + "ms");
     System.gc();
 
     resizing = false;