JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index c844315..440804b 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,19 +1,20 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * 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 
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -39,6 +40,7 @@ public class OverviewPanel extends JPanel implements Runnable
   AlignmentPanel ap;
 
   final AnnotationRenderer renderer = new AnnotationRenderer();
+
   float scalew = 1f;
 
   float scaleh = 1f;
@@ -86,7 +88,7 @@ public class OverviewPanel extends JPanel implements Runnable
     float initialScale = (float) av.getAlignment().getWidth()
             / (float) av.getAlignment().getHeight();
 
-    if (av.getAlignmentConservationAnnotation()== null)
+    if (av.getAlignmentConservationAnnotation() == null)
     {
       graphHeight = 0;
     }
@@ -115,6 +117,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addComponentListener(new ComponentAdapter()
     {
+      @Override
       public void componentResized(ComponentEvent evt)
       {
         if ((getWidth() != width)
@@ -127,6 +130,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addMouseMotionListener(new MouseMotionAdapter()
     {
+      @Override
       public void mouseDragged(MouseEvent evt)
       {
         if (!av.wrapAlignment)
@@ -142,6 +146,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent evt)
       {
         if (!av.wrapAlignment)
@@ -201,8 +206,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if (av.hasHiddenRows())
     {
-      row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
-              row);
+      row = av.getAlignment().getHiddenSequences()
+              .findIndexWithoutHiddenSeqs(row);
     }
 
     ap.setScrollValues(col, row);
@@ -242,6 +247,7 @@ public class OverviewPanel extends JPanel implements Runnable
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     miniMe = null;
@@ -296,7 +302,8 @@ public class OverviewPanel extends JPanel implements Runnable
       hiddenRow = false;
       if (av.hasHiddenRows())
       {
-        seq = av.getAlignment().getHiddenSequences().getHiddenSequence(lastrow);
+        seq = av.getAlignment().getHiddenSequences()
+                .getHiddenSequence(lastrow);
         if (seq == null)
         {
           int index = av.getAlignment().getHiddenSequences()
@@ -357,15 +364,16 @@ public class OverviewPanel extends JPanel implements Runnable
       }
     }
 
-    if (av.getAlignmentConservationAnnotation()!= null)
+    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(),
+                  av.getAlignmentConservationAnnotation().annotations,
                   (int) (sampleCol) + 1, graphHeight,
                   (int) (col * sampleCol), (int) (col * sampleCol) + 1);
           mg.translate(-col, -sequencesHeight);
@@ -392,7 +400,8 @@ public class OverviewPanel extends JPanel implements Runnable
   {
     int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
     int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
-            .getHiddenSequences().getSize()) * av.getCharHeight();
+            .getHiddenSequences().getSize())
+            * av.getCharHeight();
 
     int startRes = av.getStartRes();
     int endRes = av.getEndRes();
@@ -408,8 +417,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if (av.hasHiddenRows())
     {
-      startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(
-              startSeq);
+      startSeq = av.getAlignment().getHiddenSequences()
+              .adjustForHiddenSeqs(startSeq);
 
       endSeq = av.getAlignment().getHiddenSequences()
               .adjustForHiddenSeqs(endSeq);
@@ -442,6 +451,7 @@ public class OverviewPanel extends JPanel implements Runnable
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
     if (resizing)