X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=1e806a5cb5afaf535b76206ef2acee4719f1f46f;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=d50fcef79cb03c12a18d63b0b3ef53551f2920a0;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index d50fcef..1e806a5 100644
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -25,10 +25,10 @@ import jalview.api.ComplexAlignFile;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.io.AlignmentFileI;
+import jalview.io.AlignmentFileReaderI;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
@@ -68,7 +68,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   AlignFrame alignFrame;
 
-  AlignmentFileI source = null;
+  AlignmentFileReaderI source = null;
 
   public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {
@@ -257,8 +257,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
         if (source instanceof ComplexAlignFile)
         {
-          ColumnSelection colSel = ((ComplexAlignFile) source)
-                  .getColumnSelection();
+            HiddenColumns colSel = ((ComplexAlignFile) source)
+                    .getHiddenColumns();
           SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
                   .getHiddenSequences();
           boolean showSeqFeatures = ((ComplexAlignFile) source)