Use paintAlignment

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

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index b6e7460..2506752 100755 (executable)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -31,7 +31,7 @@ public class CutAndPasteTransfer
   boolean pdbImport = false;\r
   boolean treeImport = false;\r
   boolean annotationImport = false;\r
-  Sequence seq;\r
+  Sequence  seq;\r
   AlignFrame alignFrame;\r
 \r
   public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)\r
@@ -123,9 +123,23 @@ public class CutAndPasteTransfer
 \r
     if (pdbImport)\r
     {\r
-      new MCview.AppletPDBViewer(text, AppletFormatAdapter.PASTE,\r
-                                 seq,\r
-                                 alignFrame.getSeqcanvas());\r
+      PDBEntry pdb = new PDBEntry();\r
+      pdb.setFile(text);\r
+\r
+      if ( alignFrame.alignPanel.av.applet.jmolAvailable )\r
+        new jalview.appletgui.AppletJmol(pdb,\r
+                                         new Sequence[]\r
+                                         {seq},\r
+                                         alignFrame.alignPanel,\r
+                                         AppletFormatAdapter.PASTE);\r
+      else\r
+\r
+        new MCview.AppletPDBViewer(pdb,\r
+                                   new Sequence[]\r
+                                   {seq},\r
+                                   alignFrame.alignPanel,\r
+                                   AppletFormatAdapter.PASTE);\r
+\r
     }\r
     else if (treeImport)\r
     {\r