X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=3eced2fc89b44548f20593715a652ba96eaf4511;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=a81c998c99bcfca1f41eb06e67a0b4a50d6e826a;hpb=95ebbef7b78bf266a8252bd479510be3c80cd234;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index a81c998..3eced2f 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -28,9 +28,9 @@ import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
-import jalview.io.AlignmentFileI;
+import jalview.io.AlignmentFileReaderI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
@@ -73,7 +73,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
   AlignViewportI viewport;
 
-  AlignmentFileI source = null;
+  AlignmentFileReaderI source = null;
 
   public CutAndPasteTransfer()
   {
@@ -284,8 +284,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         AlignFrame af;
         if (source instanceof ComplexAlignFile)
         {
-          ColumnSelection colSel = ((ComplexAlignFile) source)
-                  .getColumnSelection();
+          HiddenColumns hidden = ((ComplexAlignFile) source)
+                  .getHiddenColumns();
           SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
                   .getHiddenSequences();
           boolean showSeqFeatures = ((ComplexAlignFile) source)
@@ -294,10 +294,11 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
                   .getGlobalColourScheme();
           FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                   .getDisplayedFeatures();
-          af = new AlignFrame(al, hiddenSeqs, colSel,
+          af = new AlignFrame(al, hiddenSeqs, hidden,
                   AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.getViewport().setFeaturesDisplayed(fd);
+          af.setMenusForViewport();
           ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
                   colourSchemeName, al);
           if (cs != null)