X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=1574d0350772b2e8882ebb5f29efbbd05d8155b5;hb=01a838156a865a61389825b3c5c968b6d8eee8f3;hp=c3ebd7153f026eaeb325d5e66f268dd1cf7b81b7;hpb=61aec75b49682917c6c445682aa97ce8de7344aa;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index c3ebd71..1574d03 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 +736,17 @@ public class AlignmentPanel extends GAlignmentPanel
 
       pg.setColor(currentTextColor);
 
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId
-          ( av.getShowJVSuffix());
+      int xPos = 0;
+      if (av.rightAlignIds)
+      {
+        fm = pg.getFontMetrics();
+        xPos = idWidth - fm.stringWidth(
+            seq.getDisplayId(av.getShowJVSuffix())
+            ) - 4;
+      }
 
-      pg.drawString(string, 0,
+      pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),
+                    xPos,
                     ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
                     (av.getCharHeight() / 5));
     }
@@ -802,8 +837,13 @@ public class AlignmentPanel extends GAlignmentPanel
       {
         SequenceI s = av.alignment.getSequenceAt(i);
         String string = s.getDisplayId( av.getShowJVSuffix());
-
-        pg.drawString(string, 0,
+        int xPos = 0;
+        if (av.rightAlignIds)
+        {
+          FontMetrics fm = getFontMetrics(italic);
+          xPos = idWidth - fm.stringWidth( string ) - 4;
+        }
+        pg.drawString(string, xPos,
                       ( (i * av.charHeight) + ypos + av.charHeight) -
                       (av.charHeight / 5));
       }