JAL-2388 Unit tests and tidies

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 923616f..2c77942 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.viewmodel.OverviewDimensions;
 
@@ -88,14 +89,7 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.forOverview = true;
     fr = new FeatureRenderer(alPanel);
 
-    boolean showAnnotation = true;
-    // TODO: in applet this was getSequenceConsensusHash()
-    // check if it makes any functional difference: hconsensus or conservation
-    if (av.getAlignmentConservationAnnotation() == null)
-    {
-      showAnnotation = false;
-    }
-    od = new OverviewDimensions(av.getPosProps(), showAnnotation);
+    od = new OverviewDimensions(av.getPosProps(), av.isShowAnnotation());
 
     addComponentListener(new ComponentAdapter()
     {
@@ -117,8 +111,6 @@ public class OverviewPanel extends JPanel implements Runnable
       {
         if (!av.getWrapAlignment())
         {
-          // TODO: feature: jv2.5 detect shift drag and update selection from
-          // it.
           od.updateViewportFromMouse(evt.getX(), evt.getY(), av
                   .getAlignment().getHiddenSequences(), av
                   .getColumnSelection(), av.getPosProps());
@@ -160,8 +152,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if ((getWidth() > 0) && (getHeight() > 0))
     {
-      od.setWidth(getWidth()); // width = getWidth();
-      od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
+      od.setWidth(getWidth());
+      od.setHeight(getHeight());
     }
 
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
@@ -208,7 +200,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     buildImage(sampleRow, sampleCol);
 
-    if (av.getAlignmentConservationAnnotation() != null)
+    if (av.isShowAnnotation())
     {
       renderer.updateFromAlignViewport(av);
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
@@ -239,13 +231,16 @@ public class OverviewPanel extends JPanel implements Runnable
     setBoxPosition();
   }
 
+  /*
+   * Build the overview panel image
+   */
   private void buildImage(float sampleRow, float sampleCol)
   {
     int lastcol = -1;
     int lastrow = -1;
     int color = Color.white.getRGB();
 
-    jalview.datamodel.SequenceI seq = null;
+    SequenceI seq = null;
 
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
@@ -268,12 +263,6 @@ public class OverviewPanel extends JPanel implements Runnable
         seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
       }
 
-      if (seq == null)
-      {
-        System.out.println(lastrow + " null");
-        continue;
-      }
-
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
       {
         if (doCopy)
@@ -287,9 +276,7 @@ public class OverviewPanel extends JPanel implements Runnable
           color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols,
                   lastcol);
         }
-        // else if ((int) (col * sampleCol) == lastcol && (int) (row *
-        // sampleRow) == lastrow))
-        // we just use the color we already have , so don't need to set it
+        // else we just use the color we already have , so don't need to set it
 
         miniMe.setRGB(col, row, color);
       }
@@ -304,7 +291,11 @@ public class OverviewPanel extends JPanel implements Runnable
   {
     int color;
 
-    if (seq.getLength() > lastcol)
+    if (seq == null)
+    {
+      color = Color.white.getRGB();
+    }
+    else if (seq.getLength() > lastcol)
     {
       color = sr.getResidueBoxColour(seq, lastcol).getRGB();
 
@@ -315,7 +306,7 @@ public class OverviewPanel extends JPanel implements Runnable
     }
     else
     {
-      color = Color.white.getRGB(); // White
+      color = Color.white.getRGB();
     }
 
     if (hiddenRow
@@ -367,7 +358,7 @@ public class OverviewPanel extends JPanel implements Runnable
         g.fillRect(0, 0, getWidth(), getHeight());
       }
     }
-    // TODO: render selected regions
+
     g.setColor(Color.red);
     od.drawBox(g);
   }