JAL-2491 Renamed comp scrolling flag for consistency; small tweaks

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index f0dd524..0f37544 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -21,7 +21,9 @@
 package jalview.appletgui;
 
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.ViewportListenerI;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -34,9 +36,10 @@ import java.awt.event.ComponentEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.beans.PropertyChangeEvent;
 
 public class OverviewPanel extends Panel implements Runnable,
-        MouseMotionListener, MouseListener
+        MouseMotionListener, MouseListener, ViewportListenerI
 {
   private OverviewDimensions od;
 
@@ -76,9 +79,13 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
 
-    od = new OverviewDimensions(av.getPosProps(), av.isShowAnnotation());
+    od = new OverviewDimensions(av.getRanges(),
+            (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
+
+    av.getRanges().addPropertyChangeListener(this);
+
     addComponentListener(new ComponentAdapter()
     {
 
@@ -143,8 +150,8 @@ public class OverviewPanel extends Panel implements Runnable,
   {
     od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
             .getHiddenSequences(), av.getColumnSelection(), av
-            .getPosProps());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+            .getRanges());
+    // ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
 
@@ -166,10 +173,10 @@ public class OverviewPanel extends Panel implements Runnable,
 
     resizing = true;
 
-    if ((getWidth() > 0) && (getHeight() > 0))
+    if ((getSize().width > 0) && (getSize().height > 0))
     {
-      od.setWidth(getWidth());
-      od.setHeight(getHeight());
+      od.setWidth(getSize().width);
+      od.setHeight(getSize().height);
     }
     setSize(new Dimension(od.getWidth(), od.getHeight()));
 
@@ -191,7 +198,7 @@ public class OverviewPanel extends Panel implements Runnable,
     if (getSize().width > 0 && getSize().height > 0)
     {
       od.setWidth(getSize().width);
-      od.setHeight(getSize().height - od.getGraphHeight());
+      od.setHeight(getSize().height);
     }
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
@@ -208,7 +215,9 @@ public class OverviewPanel extends Panel implements Runnable,
 
     buildImage(sampleRow, sampleCol, mg);
 
-    if (av.isShowAnnotation())
+    // check for conservation annotation to make sure overview works for DNA too
+    if (av.isShowAnnotation()
+            && (av.getAlignmentConservationAnnotation() != null))
     {
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
       {
@@ -248,6 +257,7 @@ 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 +287,7 @@ 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 +315,12 @@ 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
@@ -336,10 +337,10 @@ public class OverviewPanel extends Panel implements Runnable,
    * changed
    * 
    */
-  public void setBoxPosition()
+  private void setBoxPosition()
   {
     od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+            .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
     repaint();
   }
 
@@ -362,4 +363,10 @@ public class OverviewPanel extends Panel implements Runnable,
     }
   }
 
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    setBoxPosition();
+  }
+
 }