JAL-1115 refactor base collection for Alignment from Vector to locally synchronized...

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 4b646c3..b48b2a4 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,18 +1,18 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
+ *
  * This file is part of Jalview.
- * 
+ *
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
+ * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  * PURPOSE.  See the GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.appletgui;
@@ -67,7 +67,7 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
     fr.overview = true;
-    
+
     // scale the initial size of overviewpanel to shape of alignment
     float initialScale = (float) av.getAlignment().getWidth()
             / (float) av.getAlignment().getHeight();
@@ -102,6 +102,7 @@ public class OverviewPanel extends Panel implements Runnable,
     addComponentListener(new ComponentAdapter()
     {
 
+      @Override
       public void componentResized(ComponentEvent evt)
       {
         if (getSize().width != width
@@ -120,22 +121,27 @@ public class OverviewPanel extends Panel implements Runnable,
 
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     boxX = evt.getX();
@@ -143,6 +149,7 @@ public class OverviewPanel extends Panel implements Runnable,
     checkValid();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     boxX = evt.getX();
@@ -150,6 +157,7 @@ public class OverviewPanel extends Panel implements Runnable,
     checkValid();
   }
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     boxX = evt.getX();
@@ -242,6 +250,7 @@ public class OverviewPanel extends Panel implements Runnable,
   // the overview is being calculated
   boolean resizeAgain = false;
 
+  @Override
   public void run()
   {
     miniMe = null;
@@ -367,7 +376,7 @@ public class OverviewPanel extends Panel implements Runnable,
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
-          ap.annotationPanel.renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+          ap.annotationPanel.renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
                   (int) (sampleCol) + 1, graphHeight,
                   (int) (col * sampleCol), (int) (col * sampleCol) + 1);
           mg.translate(-col, -sequencesHeight);
@@ -435,11 +444,13 @@ public class OverviewPanel extends Panel implements Runnable,
     repaint();
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     Graphics og = offscreen.getGraphics();