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.

diff --cc src/jalview/appletgui/AlignFrame.java
index 15904df,cc2c966..90b1a05
--- 1/src/jalview/appletgui/AlignFrame.java
--- 2/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@@ -3682,22 -3681,16 +3681,28 @@@ public class AlignFrame extends Embmenu
          \r
          TCoffeeScoreFile file = TCoffeeScoreFile.load( new InputStreamReader( url.openStream() ) );\r
          if( file == null ) {\r
++       // TODO: raise a dialog box here rather than bomb out.\r
++            \r
                  throw new RuntimeException("The file provided does not match the T-Coffee scores file format");\r
          }\r
 -        // TODO add parameter to indicate if matching should be done\r
 +        \r
 +        /*\r
 +         * check that the score matrix matches the alignment dimensions\r
 +         */\r
 +        AlignmentI aln; \r
 +        if( (aln=viewport.alignment) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {\r
-                 throw new RuntimeException("The scores matrix does not match the alignment dimensions");\r
++          // TODO: raise a dialog box here rather than bomb out.\r
++          throw new RuntimeException("The scores matrix does not match the alignment dimensions");\r
++                \r
 +        }\r
 +        \r
-         tcoffeeColour.setEnabled(true);\r
-         tcoffeeScoreFile = file;\r
-         \r
-         // switch to this color\r
-         changeColour(new TCoffeeColourScheme(tcoffeeScoreFile));\r
++         // TODO add parameter to indicate if matching should be done\r
+         if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
+         {\r
+                 tcoffeeColour.setEnabled(true);\r
+                 // switch to this color\r
+                 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+           }\r
 -\r
    }\r
    \r
    \r

diff --cc src/jalview/gui/AlignFrame.java
index 3ba7319,2ba0d59..221d52c
--- 1/src/jalview/gui/AlignFrame.java
--- 2/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(

diff --cc src/jalview/io/TCoffeeScoreFile.java
Simple merge