JAL-1925 update source version in license

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index b48b2a4..dcdadf5 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,26 +1,38 @@
 /*
- * 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 2.9.0b2)
+ * 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.appletgui;
 
 import jalview.datamodel.AlignmentI;
 
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
 
 public class OverviewPanel extends Panel implements Runnable,
         MouseMotionListener, MouseListener
@@ -66,7 +78,6 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.renderGaps = false;
     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()
@@ -207,8 +218,8 @@ 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);
@@ -226,10 +237,9 @@ public class OverviewPanel extends Panel implements Runnable,
       return;
     }
 
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
-      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
-      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+      fr.transferSettings(ap.seqPanel.seqCanvas.fr);
     }
 
     resizing = true;
@@ -257,7 +267,7 @@ public class OverviewPanel extends Panel implements Runnable,
     int alwidth = av.getAlignment().getWidth();
     int alheight = av.getAlignment().getHeight();
 
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
       fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
     }
@@ -288,8 +298,10 @@ public class OverviewPanel extends Panel implements Runnable,
     Color color = Color.yellow;
     int row, col, sameRow = 0, sameCol = 0;
     jalview.datamodel.SequenceI seq;
+    final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+            .hasHiddenColumns();
     boolean hiddenRow = false;
-    AlignmentI alignment=av.getAlignment();
+    AlignmentI alignment = av.getAlignment();
     for (row = 0; row <= sequencesHeight; row++)
     {
       if ((int) (row * sampleRow) == lastrow)
@@ -299,7 +311,7 @@ public class OverviewPanel extends Panel implements Runnable,
       }
 
       hiddenRow = false;
-      if (av.hasHiddenRows())
+      if (hasHiddenRows)
       {
         seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
         if (seq == null)
@@ -334,7 +346,7 @@ public class OverviewPanel extends Panel implements Runnable,
         {
           color = sr.getResidueBoxColour(seq, lastcol);
 
-          if (av.showSequenceFeatures)
+          if (av.isShowSequenceFeatures())
           {
             color = fr.findFeatureColour(color, seq, lastcol);
           }
@@ -345,8 +357,8 @@ public class OverviewPanel extends Panel implements Runnable,
         }
 
         if (hiddenRow
-                || (av.hasHiddenColumns() && !av.getColumnSelection()
-                        .isVisible(lastcol)))
+                || (hasHiddenCols && !av.getColumnSelection().isVisible(
+                        lastcol)))
         {
           color = color.darker().darker();
         }
@@ -369,14 +381,16 @@ 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);
@@ -400,7 +414,8 @@ 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();
@@ -416,8 +431,8 @@ 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);