Copy works with selection area

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 05ba50c..0edc578 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -362,6 +362,7 @@ public class AlignFrame
           omitHidden) ;\r
 \r
 \r
+\r
       if (output == null)\r
       {\r
         return false;\r
@@ -667,15 +668,8 @@ public class AlignFrame
     {\r
       return;\r
     }\r
-    SequenceI [] seqs;\r
-    if(viewport.getSelectionGroup()==null)\r
-    {\r
-      seqs = viewport.alignment.getSequencesArray();\r
-    }\r
-    else\r
-    {\r
-      seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.alignment);\r
-    }\r
+\r
+    SequenceI [] seqs = viewport.getSelectionAsNewSequence();\r
 \r
     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 \r
@@ -2385,9 +2379,9 @@ public class AlignFrame
       if (nf.getTree() != null)\r
       {\r
         tp = new TreePanel(viewport,\r
-                           nf,\r
                            "FromFile",\r
-                           title);\r
+                           title,\r
+                           nf);\r
 \r
         tp.setSize(w,h);\r
 \r