JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 5df60d2..9397ceb 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,10 +22,17 @@ package jalview.gui;
 
 import jalview.renderer.AnnotationRenderer;
 
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JPanel;
 
 /**
  * DOCUMENT ME!
@@ -85,7 +92,7 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.renderGaps = false;
     sr.forOverview = true;
     fr = new FeatureRenderer(ap);
-    
+
     // scale the initial size of overviewpanel to shape of alignment
     float initialScale = (float) av.getAlignment().getWidth()
             / (float) av.getAlignment().getHeight();
@@ -135,7 +142,7 @@ public class OverviewPanel extends JPanel implements Runnable
       @Override
       public void mouseDragged(MouseEvent evt)
       {
-        if (!av.wrapAlignment)
+        if (!av.getWrapAlignment())
         {
           // TODO: feature: jv2.5 detect shift drag and update selection from
           // it.
@@ -151,7 +158,7 @@ public class OverviewPanel extends JPanel implements Runnable
       @Override
       public void mousePressed(MouseEvent evt)
       {
-        if (!av.wrapAlignment)
+        if (!av.getWrapAlignment())
         {
           boxX = evt.getX();
           boxY = evt.getY();
@@ -285,6 +292,8 @@ public class OverviewPanel extends JPanel implements Runnable
     int color = Color.white.getRGB();
     int row, col;
     jalview.datamodel.SequenceI seq;
+    final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+            .hasHiddenColumns();
     boolean hiddenRow = false;
     for (row = 0; row < sequencesHeight; row++)
     {
@@ -302,7 +311,7 @@ public class OverviewPanel extends JPanel implements Runnable
       lastrow = (int) (row * sampleRow);
 
       hiddenRow = false;
-      if (av.hasHiddenRows())
+      if (hasHiddenRows)
       {
         seq = av.getAlignment().getHiddenSequences()
                 .getHiddenSequence(lastrow);
@@ -355,8 +364,8 @@ public class OverviewPanel extends JPanel implements Runnable
         }
 
         if (hiddenRow
-                || (av.hasHiddenColumns() && !av.getColumnSelection()
-                        .isVisible(lastcol)))
+                || (hasHiddenCols && !av.getColumnSelection().isVisible(
+                        lastcol)))
         {
           color = new Color(color).darker().darker().getRGB();
         }