X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=9c23a0af68dd02273967ac7632163da45ae57925;hb=b78f02f944e0cf69ba6cfe14a165d6ad210e45dd;hp=0cba50e2c0d7a38de82730397bbdc1c337a00d47;hpb=691798cf6a90094f4c83e79fd5c703457b1135b0;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 0cba50e..9c23a0a 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -492,6 +492,8 @@ public class JalviewLite extends Applet implements
       boolean seqlimits = suffix.equalsIgnoreCase("true");
       if (alf.viewport.getSelectionGroup() != null)
       {
+        // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data
+        // TODO consider using getSequenceSelection instead here
         String reply = new AppletFormatAdapter().formatSequences(format,
                 new Alignment(alf.viewport.getSelectionAsNewSequence()),
                 seqlimits);
@@ -730,9 +732,9 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
-  public void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
+  public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
   {
-    alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);
+    return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);
   }
 
 
@@ -1821,8 +1823,7 @@ public class JalviewLite extends Applet implements
 
         if (protocol == jalview.io.AppletFormatAdapter.PASTE)
         {
-          newAlignFrame.setTitle("Sequences from "
-                  + applet.getDocumentBase());
+          newAlignFrame.setTitle("Sequences from " + applet.getDocumentBase());
         }
 
         newAlignFrame.statusBar.setText("Successfully loaded file " + file);
@@ -1863,6 +1864,25 @@ public class JalviewLite extends Applet implements
           }
         }
 
+
+        /*
+         * Try to load T-Coffee score file
+         */
+        String sScoreFile = applet.getParameter("scoreFile");
+        if( sScoreFile != null && !"".equals(sScoreFile) ) {
+            try {
+              if (debug) {
+                System.err.println("Attempting to load T-COFFEE score file from the scoreFile parameter");
+              }
+              if (!newAlignFrame.loadScoreFile(sScoreFile)) {
+                System.err.println("Failed to parse T-COFFEE parameter as a valid score file ('"+sScoreFile+"')");
+              }
+            }catch( Exception e ) {
+            	System.err.printf("Cannot read score file: '%s'. Cause: %s \n", sScoreFile, e.getMessage());
+            }
+        }
+       
+
         // ///////////////////////////
         // modify display of features
         // we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed