X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=90b1a0507aed65faa06126154490b255856f7af9;hb=6a3f4318037072a77588afb951a5a53835d5da99;hp=c1dbf303c2923abee49fb2e73252531e9e5264a7;hpb=34d8b4dc08dcd27c3b5ac3bf7811f709b4db5938;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index c1dbf30..90b1a05 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -100,7 +100,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 
   String jalviewServletURL;
   
-  TCoffeeScoreFile tcoffeeScoreFile;
 
   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
   {
@@ -998,7 +997,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       changeColour(new Blosum62ColourScheme());
     }
     else if (source == tcoffeeColour) {
-        changeColour(new TCoffeeColourScheme(tcoffeeScoreFile));
+        changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
     }
     else if (source == annotationColour)
     {
@@ -2335,7 +2334,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         {
           try
           {
-            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+            sg.cs = cs.getClass().newInstance();
           } catch (Exception ex)
           {
             ex.printStackTrace();
@@ -3682,14 +3681,28 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 	  
 	  TCoffeeScoreFile file = TCoffeeScoreFile.load( new InputStreamReader( url.openStream() ) );
 	  if( file == 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");
 	  }
 	  
-	  tcoffeeColour.setEnabled(true);
-	  tcoffeeScoreFile = file;
+	  /*
+	   * check that the score matrix matches the alignment dimensions
+	   */
+	  AlignmentI aln; 
+	  if( (aln=viewport.alignment) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
+	    // TODO: raise a dialog box here rather than bomb out.
+	    throw new RuntimeException("The scores matrix does not match the alignment dimensions");
+		  
+	  }
 	  
-	  // switch to this color
-	  changeColour(new TCoffeeColourScheme(tcoffeeScoreFile));
+	   // TODO add parameter to indicate if matching should be done
+	  if (file.annotateAlignment(alignPanel.getAlignment(), false))
+	  {
+	          tcoffeeColour.setEnabled(true);
+	          // switch to this color
+	          changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+          }
   }