X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=0012ec4765e6141429592ef6541c287c6c5ffcf8;hb=e5f2de91dc41062d8cee8a2a900710f63cf5ae42;hp=bd87bb2d7d7718a3928fb26b0c9d09d1607aa853;hpb=f3bc67915e61855d87866b4a614fe7a953813408;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index bd87bb2..0012ec4 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -27,10 +27,10 @@ import jalview.schemes.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
-
 import java.io.*;
-
 import javax.swing.*;
+import java.beans.*;
+
 
 
 /**
@@ -96,11 +96,39 @@ public class AlignmentPanel extends GAlignmentPanel
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
+    final AlignmentPanel ap = this;
+    av.addPropertyChangeListener(new PropertyChangeListener()
+    {
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        if (evt.getPropertyName().equals("alignment"))
+        {
+          PaintRefresher.Refresh(ap,
+                                 av.getSequenceSetId(),
+                                 true,
+                                 true);
+          alignmentChanged();
+        }
+      }
+      });
 
     adjustAnnotationHeight();
 
   }
 
+  public void alignmentChanged()
+  {
+    av.alignmentChanged(this);
+
+    if (overviewPanel != null)
+      overviewPanel.updateOverviewImage();
+
+    alignFrame.updateEditMenuBar();
+
+    repaint();
+  }
+
+
 
   /**
    * DOCUMENT ME!
@@ -285,7 +313,6 @@ public class AlignmentPanel extends GAlignmentPanel
         annotationSpaceFillerHolder.getWidth(),
         height));
 
-    annotationPanel.repaint();
     repaint();
   }
 
@@ -687,18 +714,19 @@ public class AlignmentPanel extends GAlignmentPanel
     pg.setFont(new Font(av.getFont().getName(),
                         Font.ITALIC,
                         av.getFont().getSize()));
+    SequenceI seq;
     for (int i = startSeq; i < endSeq; i++)
     {
+      seq = av.getAlignment().getSequenceAt(i);
       if ( (av.getSelectionGroup() != null) &&
-          av.getSelectionGroup().getSequences(false).contains(
-              av.getAlignment().getSequenceAt(i)))
+          av.getSelectionGroup().getSequences(false).contains(seq))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
       }
       else
       {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
+        currentColor = av.getSequenceColour(seq);
         currentTextColor = Color.black;
       }
 
@@ -708,10 +736,8 @@ public class AlignmentPanel extends GAlignmentPanel
 
       pg.setColor(currentTextColor);
 
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId
-          ( av.getShowJVSuffix());
-
-      pg.drawString(string, 0,
+      pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),
+                    0,
                     ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
                     (av.getCharHeight() / 5));
     }
@@ -873,6 +899,9 @@ public class AlignmentPanel extends GAlignmentPanel
       height += annotationPanel.adjustPanelHeight() + 3;
     }
 
+    try
+    {
+
     jalview.util.ImageMaker im;
     if(type==jalview.util.ImageMaker.PNG)
       im  = new jalview.util.ImageMaker(this,
@@ -885,8 +914,6 @@ public class AlignmentPanel extends GAlignmentPanel
                                        "Create EPS file from alignment",
                                         width, height, file, alignFrame.getTitle() );
 
-    try
-    {
       if (av.getWrapAlignment())
       {
         if(im.getGraphics()!=null)