JAL-1065 JAL-1066 - refactored tcoffee score-> jalview vis object code to a create...

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index c1dbf30..cc2c966 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -100,7 +100,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 \r
   String jalviewServletURL;\r
   \r
-  TCoffeeScoreFile tcoffeeScoreFile;\r
 \r
   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)\r
   {\r
@@ -998,7 +997,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       changeColour(new Blosum62ColourScheme());\r
     }\r
     else if (source == tcoffeeColour) {\r
-        changeColour(new TCoffeeColourScheme(tcoffeeScoreFile));\r
+        changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
     }\r
     else if (source == annotationColour)\r
     {\r
@@ -3684,12 +3683,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
          if( file == null ) {\r
                  throw new RuntimeException("The file provided does not match the T-Coffee scores file format");\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