X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;fp=src%2Fjalview%2Fgui%2FAlignFrame.java;h=221d52c4918642cb15933a1e34284041fda6044d;hb=6a3f4318037072a77588afb951a5a53835d5da99;hp=3ba73192be43525bca54f8dce58871939b09e35b;hpb=1379350f04bc63ca05bd428afb86717c4764755d;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3ba7319..221d52c 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -143,8 +143,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   Vector alignPanels = new Vector();
   
-  TCoffeeScoreFile tcoffeeScoreFile;
-
   /**
    * Last format used to load or save alignments in this window
    */
@@ -3884,6 +3882,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 	      {
 	    	  TCoffeeScoreFile result = TCoffeeScoreFile.load(new File(sFilePath));
 	    	  if( result == null ) { 
+	    	       // TODO: raise a dialog box here rather than bomb out.
+	    	  
 	    		  throw new RuntimeException("The file provided does not match the T-Coffee scores file format"); 
 	    	  }
 
@@ -3892,14 +3892,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 	    	   */
 	    	  AlignmentI aln; 
 	    	  if( (aln=viewport.alignment) != null && (aln.getHeight() != result.getHeight() || aln.getWidth() != result.getWidth()) ) {
-	    		  throw new RuntimeException("The scores matrix does not match the alignment dimensions");
+	    	      // TODO: raise a dialog box here rather than bomb out.
+	    	    throw new RuntimeException("The scores matrix does not match the alignment dimensions");
 	    	  }
-
-	    	  changeColour( new TCoffeeColourScheme(result) );
-	    	  tcoffeeScoreFile = result;
-	    	  tcoffeeColour.setEnabled(true);
-	      	  tcoffeeColour.setSelected(true);
-	    	  
+	          if (result.annotateAlignment(alignPanel.getAlignment(), true))
+	          {
+	                  tcoffeeColour.setEnabled(true);
+	                  tcoffeeColour.setSelected(true);
+	                  // switch to this color
+	                  changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+	          } else {
+	            tcoffeeColour.setEnabled(false);
+	            tcoffeeColour.setSelected(false);
+	          }
 	      } 
 	      catch (Exception ex) {
 	        JOptionPane.showMessageDialog(
@@ -3917,9 +3922,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   
   @Override
   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) {
-	  if( tcoffeeScoreFile != null ) {
-    	  changeColour( new TCoffeeColourScheme(tcoffeeScoreFile) );
-	  }
+	  changeColour( new TCoffeeColourScheme(alignPanel.getAlignment()) );
   }
   
 //  /**