From 0365a951ffb7cdab64e2f0872b4b719c910527ad Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 4 Nov 2004 17:55:51 +0000
Subject: [PATCH] Allowed for addition of OverviewPanel

---
 src/jalview/gui/AlignmentPanel.java |   47 ++++++++++++++++++++++++++++++++---
 1 file changed, 43 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index cf3e3df..df0459f 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -2,13 +2,14 @@ package jalview.gui;
 
 import jalview.jbgui.GAlignmentPanel;
 import java.awt.*;
-import javax.swing.*;
 import java.awt.event.*;
+import java.io.*;
 
 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener
 {
 
   AlignViewport     av;
+  OverviewPanel overviewPanel;
   public SeqPanel   seqPanel;
   public IdPanel    idPanel;
   public AlignFrame alignFrame;
@@ -26,7 +27,9 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     scalePanel = new ScalePanel(av);
     scorePanel = new ScorePanel(av);
 
+
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
+    idPanel.addNotify();
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
     scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
@@ -39,7 +42,10 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     addComponentListener(new ComponentAdapter()
    {
        public void componentResized(ComponentEvent evt)
-     {      RefreshPanels();    }
+     {
+     //  if(!initialising)
+     RefreshPanels();
+     }
    });
 
   }
@@ -63,6 +69,15 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     }
   }
 
+ public OverviewPanel getOverviewPanel()
+ {
+   return overviewPanel;
+ }
+
+ public void setOverviewPanel(OverviewPanel op)
+ {
+   overviewPanel = op;
+ }
 
 
   public void setGraphPanelVisible(boolean b)
@@ -72,18 +87,34 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     RefreshPanels();
   }
 
+  public void setColourScheme(jalview.schemes.ColourSchemeI cs)
+  {
+    seqPanel.setColourScheme(cs);
+    if(overviewPanel!=null)
+      overviewPanel.updateOverviewImage();
+  }
 
 
   public void RefreshPanels()
   {
+
+  /*  try{
+      ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream("dump.dat"));
+      out.writeObject( (jalview.datamodel.Alignment)av.getAlignment() );
+    }catch(IOException ex){ex.printStackTrace();}*/
+
     invalidate();
-    idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
     validate();
     idPanel.idCanvas.paintFlag = true;
+    idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
     seqPanel.seqCanvas.paintFlag = true;
     setScrollValues(av.getStartRes(), av.getStartSeq());
     av.getConsensus(true);
     repaint();
+
+    if(overviewPanel!=null)
+      overviewPanel.updateOverviewImage();
+
   }
 
   int hextent = 0;
@@ -108,11 +139,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
+    seqPanel.seqCanvas.paintFlag = true;
+    repaint();
 
   }
 
 
-  public void adjustmentValueChanged(AdjustmentEvent evt) {
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
 
     if (evt.getSource() == hscroll)
     {
@@ -128,6 +162,11 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
         av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());
     }
 
+
+    if(overviewPanel!=null)
+      overviewPanel.setBoxPosition();
+
+
     repaint();
   }
 
-- 
1.7.10.2