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 475f0c7..9397ceb 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,32 +1,42 @@
 /*
- * 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 2.9)
+ * Copyright (C) 2015 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
+ * 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/>.
+ * 
+ * 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;
 
 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!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -39,6 +49,7 @@ public class OverviewPanel extends JPanel implements Runnable
   AlignmentPanel ap;
 
   final AnnotationRenderer renderer = new AnnotationRenderer();
+
   float scalew = 1f;
 
   float scaleh = 1f;
@@ -63,11 +74,11 @@ public class OverviewPanel extends JPanel implements Runnable
   // main visible SeqCanvas
   SequenceRenderer sr;
 
-  FeatureRenderer fr;
+  jalview.renderer.seqfeatures.FeatureRenderer fr;
 
   /**
    * Creates a new OverviewPanel object.
-   *
+   * 
    * @param ap
    *          DOCUMENT ME!
    */
@@ -86,7 +97,7 @@ 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;
     }
@@ -131,7 +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.
@@ -147,7 +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();
@@ -204,8 +215,8 @@ 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);
@@ -250,9 +261,9 @@ public class OverviewPanel extends JPanel implements Runnable
   {
     miniMe = null;
 
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+      fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
     }
 
     int alwidth = av.getAlignment().getWidth();
@@ -281,6 +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++)
     {
@@ -298,9 +311,10 @@ public class OverviewPanel extends JPanel implements Runnable
       lastrow = (int) (row * sampleRow);
 
       hiddenRow = false;
-      if (av.hasHiddenRows())
+      if (hasHiddenRows)
       {
-        seq = av.getAlignment().getHiddenSequences().getHiddenSequence(lastrow);
+        seq = av.getAlignment().getHiddenSequences()
+                .getHiddenSequence(lastrow);
         if (seq == null)
         {
           int index = av.getAlignment().getHiddenSequences()
@@ -339,7 +353,7 @@ public class OverviewPanel extends JPanel implements Runnable
         {
           color = sr.getResidueBoxColour(seq, lastcol).getRGB();
 
-          if (av.showSequenceFeatures)
+          if (av.isShowSequenceFeatures())
           {
             color = fr.findFeatureColour(color, seq, lastcol);
           }
@@ -350,8 +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();
         }
@@ -361,7 +375,7 @@ public class OverviewPanel extends JPanel implements Runnable
       }
     }
 
-    if (av.getAlignmentConservationAnnotation()!= null)
+    if (av.getAlignmentConservationAnnotation() != null)
     {
       renderer.updateFromAlignViewport(av);
       for (col = 0; col < width; col++)
@@ -369,7 +383,8 @@ public class OverviewPanel extends JPanel implements Runnable
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
-          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
+          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+                  av.getAlignmentConservationAnnotation().annotations,
                   (int) (sampleCol) + 1, graphHeight,
                   (int) (col * sampleCol), (int) (col * sampleCol) + 1);
           mg.translate(-col, -sequencesHeight);
@@ -396,7 +411,8 @@ 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();
@@ -412,8 +428,8 @@ 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);
@@ -442,7 +458,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param g
    *          DOCUMENT ME!
    */