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 342ff4c..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
@@ -1871,12 +1871,13 @@ public class JalviewLite extends Applet implements
         String sScoreFile = applet.getParameter("scoreFile");\r
         if( sScoreFile != null && !"".equals(sScoreFile) ) {\r
             try {\r
-               URL urlScore = new URL(sScoreFile);\r
-               newAlignFrame.loadScoreFile(urlScore);\r
-               \r
-            }\r
-            catch( Exception e ) {\r
-               // TODO error message log (shows a warning dialogbox?)\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