X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=5df60d2d44a9b776107f06405c488475952b4b0e;hb=2273eba5668e5340354da60fed329c6c716cc439;hp=c844315a41da24e1da5948bf738a93eddf4f5273;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index c844315..5df60d2 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/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 2.8.2)
+ * 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.
- * 
+ * 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;
 
@@ -39,6 +42,7 @@ public class OverviewPanel extends JPanel implements Runnable
   AlignmentPanel ap;
 
   final AnnotationRenderer renderer = new AnnotationRenderer();
+
   float scalew = 1f;
 
   float scaleh = 1f;
@@ -63,7 +67,7 @@ public class OverviewPanel extends JPanel implements Runnable
   // main visible SeqCanvas
   SequenceRenderer sr;
 
-  FeatureRenderer fr;
+  jalview.renderer.seqfeatures.FeatureRenderer fr;
 
   /**
    * Creates a new OverviewPanel object.
@@ -81,12 +85,12 @@ 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();
 
-    if (av.getAlignmentConservationAnnotation()== null)
+    if (av.getAlignmentConservationAnnotation() == null)
     {
       graphHeight = 0;
     }
@@ -115,6 +119,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addComponentListener(new ComponentAdapter()
     {
+      @Override
       public void componentResized(ComponentEvent evt)
       {
         if ((getWidth() != width)
@@ -127,6 +132,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addMouseMotionListener(new MouseMotionAdapter()
     {
+      @Override
       public void mouseDragged(MouseEvent evt)
       {
         if (!av.wrapAlignment)
@@ -142,6 +148,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent evt)
       {
         if (!av.wrapAlignment)
@@ -201,8 +208,8 @@ 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);
@@ -242,13 +249,14 @@ public class OverviewPanel extends JPanel implements Runnable
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     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();
@@ -296,7 +304,8 @@ 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()
@@ -335,7 +344,7 @@ 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);
           }
@@ -357,15 +366,16 @@ 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 +402,8 @@ 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 +419,8 @@ 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 +453,7 @@ public class OverviewPanel extends JPanel implements Runnable
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
     if (resizing)