JAL-958 store/recover normalised flag

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

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 311e48d..9c23a0a 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -732,9 +732,9 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame\r
    * , java.lang.String)\r
    */\r
-  public void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)\r
+  public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)\r
   {\r
-    alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);\r
+    return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);\r
   }\r
 \r
 \r
@@ -1823,8 +1823,7 @@ 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
@@ -1865,6 +1864,25 @@ 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
+              if (debug) {\r
+                System.err.println("Attempting to load T-COFFEE score file from the scoreFile parameter");\r
+              }\r
+              if (!newAlignFrame.loadScoreFile(sScoreFile)) {\r
+                System.err.println("Failed to parse T-COFFEE parameter as a valid score file ('"+sScoreFile+"')");\r
+              }\r
+            }catch( Exception e ) {\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