JAL-1065 - Visualize T-Coffee quality scores for an alignment

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 0cba50e..5785ed1 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1821,8 +1821,7 @@ public class JalviewLite extends Applet implements
 \r
         if (protocol == jalview.io.AppletFormatAdapter.PASTE)\r
         {\r
-          newAlignFrame.setTitle("Sequences from "\r
-                  + applet.getDocumentBase());\r
+          newAlignFrame.setTitle("Sequences from " + applet.getDocumentBase());\r
         }\r
 \r
         newAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
@@ -1863,6 +1862,25 @@ public class JalviewLite extends Applet implements
           }\r
         }\r
 \r
+\r
+        /*\r
+         * Try to load T-Coffee score file\r
+         */\r
+        String sScoreFile = applet.getParameter("scoreFile");\r
+        if( sScoreFile != null && !"".equals(sScoreFile) ) {\r
+            try {\r
+               URL urlScore = new URL(sScoreFile);\r
+               newAlignFrame.loadScoreFile(urlScore);\r
+               //TODO check the scores matrix matches the MSA dimensions\r
+               \r
+            }\r
+            catch( Exception e ) {\r
+               // TODO error message log (shows a warning dialogbox?)\r
+               System.err.printf("Cannot read score file: '%s'. Cause: %s \n", sScoreFile, e.getMessage());\r
+            }\r
+        }\r
+       \r
+\r
         // ///////////////////////////\r
         // modify display of features\r
         // we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed\r