JAL-1620 version bump and release notes

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index ba066a1..3d5bd1b 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,19 +1,22 @@
 /*
- * 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 2.8.2b1)
+ * 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.
- * 
+ * 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/>.
+ * 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.appletgui;
 
@@ -67,7 +70,7 @@ 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 +105,7 @@ public class OverviewPanel extends Panel implements Runnable,
     addComponentListener(new ComponentAdapter()
     {
 
+      @Override
       public void componentResized(ComponentEvent evt)
       {
         if (getSize().width != width
@@ -120,22 +124,27 @@ 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 +152,7 @@ public class OverviewPanel extends Panel implements Runnable,
     checkValid();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     boxX = evt.getX();
@@ -150,6 +160,7 @@ public class OverviewPanel extends Panel implements Runnable,
     checkValid();
   }
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     boxX = evt.getX();
@@ -199,8 +210,8 @@ public class OverviewPanel extends Panel implements Runnable,
 
     if (av.hasHiddenRows())
     {
-      row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
-              row);
+      row = av.getAlignment().getHiddenSequences()
+              .findIndexWithoutHiddenSeqs(row);
     }
 
     ap.setScrollValues(col, row);
@@ -242,6 +253,7 @@ public class OverviewPanel extends Panel implements Runnable,
   // the overview is being calculated
   boolean resizeAgain = false;
 
+  @Override
   public void run()
   {
     miniMe = null;
@@ -280,7 +292,7 @@ public class OverviewPanel extends Panel implements Runnable,
     int row, col, sameRow = 0, sameCol = 0;
     jalview.datamodel.SequenceI seq;
     boolean hiddenRow = false;
-    AlignmentI alignment=av.getAlignment();
+    AlignmentI alignment = av.getAlignment();
     for (row = 0; row <= sequencesHeight; row++)
     {
       if ((int) (row * sampleRow) == lastrow)
@@ -360,14 +372,16 @@ public class OverviewPanel extends Panel implements Runnable,
       sameRow = 1;
     }
 
-    if (av.getAlignmentConservationAnnotation()!= null)
+    if (av.getAlignmentConservationAnnotation() != null)
     {
       for (col = 0; col < width; col++)
       {
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
-          ap.annotationPanel.renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
+          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);
@@ -391,7 +405,8 @@ public class OverviewPanel extends Panel 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();
@@ -407,8 +422,8 @@ public class OverviewPanel extends Panel implements Runnable,
 
     if (av.hasHiddenRows())
     {
-      startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(
-              startSeq);
+      startSeq = av.getAlignment().getHiddenSequences()
+              .adjustForHiddenSeqs(startSeq);
 
       endSeq = av.getAlignment().getHiddenSequences()
               .adjustForHiddenSeqs(endSeq);
@@ -435,11 +450,13 @@ 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();