X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=0bb939230217c52932d03ee5becfd469e8670468;hb=2a1ff16b273585d8cefe5d799a8c1e1cee20404f;hp=743d217fb10508d7b98de06e91473040b40a3156;hpb=aa6643d51133a8541dcbe30191b344aa09907a5f;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 743d217..0bb9392 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -75,7 +75,15 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
 
-    od = new OverviewDimensions(av);
+    boolean showAnnotation = false;
+    // TODO: in applet this was getSequenceConsensusHash()
+    // check if it makes any functional difference: hconsensus or conservation
+    if (av.getAlignmentConservationAnnotation() == null)
+    {
+      showAnnotation = true;
+    }
+
+    od = new OverviewDimensions(av, showAnnotation);
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
     addComponentListener(new ComponentAdapter()
@@ -123,33 +131,24 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    od.setBoxX(evt.getX());
-    od.setBoxY(evt.getY());
-    checkValid();
+    mouseAction(evt);
   }
 
   @Override
   public void mouseReleased(MouseEvent evt)
   {
-    od.setBoxX(evt.getX());
-    od.setBoxY(evt.getY());
-    checkValid();
+    mouseAction(evt);
   }
 
   @Override
   public void mouseDragged(MouseEvent evt)
   {
-    od.setBoxX(evt.getX());
-    od.setBoxY(evt.getY());
-    checkValid();
+    mouseAction(evt);
   }
 
-  /**
-   * Check box dimensions and scroll positions and correct if necessary
-   */
-  private void checkValid()
+  private void mouseAction(MouseEvent evt)
   {
-    od.checkValid();
+    od.updateViewportFromMouse(evt.getX(), evt.getY());
     ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
@@ -207,11 +206,10 @@ public class OverviewPanel extends Panel implements Runnable,
 
     Graphics mg = miniMe.getGraphics();
 
-    od.updateScales();
+    // od.updateScales();
 
     int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
+    int alheight = av.getAlignment().getAbsoluteHeight();
     float sampleCol = alwidth / (float) od.getWidth();
     float sampleRow = alheight / (float) od.getSequencesHeight();
 
@@ -254,7 +252,7 @@ public class OverviewPanel extends Panel implements Runnable,
     int sameCol = 0;
 
     jalview.datamodel.SequenceI seq = null;
-    final boolean hasHiddenRows = av.hasHiddenRows();
+
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
 
@@ -263,33 +261,13 @@ public class OverviewPanel extends Panel implements Runnable,
       if ((int) (row * sampleRow) == lastrow)
       {
         sameRow++;
-        continue;
       }
       else
       {
-        // this should largely be a method in Alignment
-        hiddenRow = false;
-        if (hasHiddenRows)
-        {
-          seq = av.getAlignment().getHiddenSequences()
-                  .getHiddenSequence(lastrow);
-          if (seq == null)
-          {
-            int index = av.getAlignment().getHiddenSequences()
-                    .findIndexWithoutHiddenSeqs(lastrow);
-
-            seq = av.getAlignment().getSequenceAt(index);
-          }
-          else
-          {
-            hiddenRow = true;
-          }
-        }
-        else
-        {
-          seq = av.getAlignment().getSequenceAt(lastrow);
-        }
-        // end of Alignment method
+        // get the sequence which would be at alignment index 'lastrow' if no
+        // columns were hidden, and determine whether it is hidden or not
+        hiddenRow = av.getAlignment().isHidden(lastrow);
+        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
 
         for (int col = 0; col < od.getWidth(); col++)
         {
@@ -383,10 +361,7 @@ public class OverviewPanel extends Panel implements Runnable,
     {
       og.drawImage(miniMe, 0, 0, this);
       og.setColor(Color.red);
-      og.drawRect(od.getBoxX(), od.getBoxY(), od.getBoxWidth(),
-              od.getBoxHeight());
-      og.drawRect(od.getBoxX() + 1, od.getBoxY() + 1, od.getBoxWidth() - 2,
-              od.getBoxHeight() - 2);
+      od.drawBox(og);
       g.drawImage(offscreen, 0, 0, this);
     }
   }