From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 4 May 2012 16:08:21 +0000 (+0100)
Subject: Merge branch 'test_paolo_JAL-1065' into Tcoffee_JAL-1065
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6a3f4318037072a77588afb951a5a53835d5da99;p=jalview.git

Merge branch 'test_paolo_JAL-1065' into Tcoffee_JAL-1065

Conflicts:
	src/jalview/appletgui/AlignFrame.java
	src/jalview/gui/AlignFrame.java
updated handler methods for creating colourscheme for new 'jalviewish' approach to storing tcoffee scores.
---

6a3f4318037072a77588afb951a5a53835d5da99
diff --cc src/jalview/appletgui/AlignFrame.java
index 15904df,cc2c966..90b1a05
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@@ -3682,22 -3681,16 +3681,28 @@@ public class AlignFrame extends Embmenu
  	  
  	  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");
  	  }
 -	  // TODO add parameter to indicate if matching should be done
 +	  
 +	  /*
 +	   * check that the score matrix matches the alignment dimensions
 +	   */
 +	  AlignmentI aln; 
 +	  if( (aln=viewport.alignment) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.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");
++		  
 +	  }
 +	  
- 	  tcoffeeColour.setEnabled(true);
- 	  tcoffeeScoreFile = file;
- 	  
- 	  // 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()));
+           }
 -
    }
    
    
diff --cc src/jalview/gui/AlignFrame.java
index 3ba7319,2ba0d59..221d52c
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -3883,23 -3881,19 +3881,30 @@@ public class AlignFrame extends GAlignF
  	      try 
  	      {
  	    	  TCoffeeScoreFile result = TCoffeeScoreFile.load(new File(sFilePath));
 -	    	  if( result == null ) { throw new RuntimeException("The file provided does not match the T-Coffee scores file format"); }
 -
 -	    	  // TODO check that the loaded scores matches the current MSA 'dimension'
 +	    	  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"); 
 +	    	  }
 +
 +	    	  /*
 +	    	   * check that the score matrix matches the alignment dimensions
 +	    	   */
 +	    	  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(