File Parsing returns Alignments, not Sequence[]

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

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 86f55b8..bbbefa1 100755 (executable)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -124,18 +124,18 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
     }\r
     else if(alignFrame!=null)\r
     {\r
-      SequenceI[] sequences = null;\r
+      Alignment al = null;\r
 \r
       String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);\r
       try{\r
-        sequences = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE, format);\r
+        al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE, format);\r
       }catch(java.io.IOException ex)\r
       {\r
         ex.printStackTrace();\r
       }\r
-      if (sequences != null)\r
+      if (al != null)\r
       {\r
-        AlignFrame af = new AlignFrame(new Alignment(sequences), alignFrame.viewport.applet,\r
+        AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,\r
                                        "Cut & Paste input - " + format,\r
                                        false);\r
         af.statusBar.setText("Successfully pasted alignment file");\r