JAL-967, JAL-1114, JAL-1115 - modified render and calculation api to work on bare...

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index c844315..475f0c7 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/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.gui;
@@ -26,7 +26,7 @@ import javax.swing.*;
 
 /**
  * DOCUMENT ME!
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -67,7 +67,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
   /**
    * Creates a new OverviewPanel object.
-   * 
+   *
    * @param ap
    *          DOCUMENT ME!
    */
@@ -115,6 +115,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addComponentListener(new ComponentAdapter()
     {
+      @Override
       public void componentResized(ComponentEvent evt)
       {
         if ((getWidth() != width)
@@ -127,6 +128,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addMouseMotionListener(new MouseMotionAdapter()
     {
+      @Override
       public void mouseDragged(MouseEvent evt)
       {
         if (!av.wrapAlignment)
@@ -142,6 +144,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent evt)
       {
         if (!av.wrapAlignment)
@@ -242,6 +245,7 @@ public class OverviewPanel extends JPanel implements Runnable
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     miniMe = null;
@@ -359,13 +363,13 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if (av.getAlignmentConservationAnnotation()!= null)
     {
-      renderer.updateFromAlignViewport(av); 
+      renderer.updateFromAlignViewport(av);
       for (col = 0; col < width; col++)
       {
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
-          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
                   (int) (sampleCol) + 1, graphHeight,
                   (int) (col * sampleCol), (int) (col * sampleCol) + 1);
           mg.translate(-col, -sequencesHeight);
@@ -438,10 +442,11 @@ public class OverviewPanel extends JPanel implements Runnable
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
     if (resizing)