JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses...

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

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 1fdbed8..535dc62 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -23,7 +23,6 @@ package jalview.appletgui;
 import jalview.analysis.AlignmentUtils;
 import jalview.api.ComplexAlignFile;
 import jalview.bin.JalviewLite;
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
@@ -221,11 +220,11 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
   protected void loadAlignment(String text, boolean newWindow,
           AlignViewport viewport)
   {
-    Alignment al = null;
+    AlignmentI al = null;
 
     String format = new IdentifyFile().Identify(text,
             AppletFormatAdapter.PASTE);
-    AppletFormatAdapter afa = new AppletFormatAdapter(viewport);
+    AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel);
     try
     {
       al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
@@ -294,7 +293,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
    * @param al
    * @return
    */
-  protected boolean openSplitFrame(Alignment al, String format)
+  protected boolean openSplitFrame(AlignmentI al, String format)
   {
     final AlignmentI thisAlignment = this.alignFrame.getAlignViewport().getAlignment();
     if (thisAlignment.isNucleotide() == al.isNucleotide())