X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=979d1aa0f4b274e2a286028d34efd292918e714f;hb=58399507cc82e8c7940a8500af73c3ed1bdd720d;hp=f3c4d87a985e94ecd79ce6fd9276a643a3e1e4e5;hpb=bd37e6102cbb5e5a2e12d8375ece436cbfbb1bc2;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index f3c4d87..979d1aa 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -20,6 +20,22 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
 import java.awt.Toolkit;
 import java.awt.datatransfer.Clipboard;
 import java.awt.datatransfer.DataFlavor;
@@ -34,19 +50,6 @@ import javax.swing.JOptionPane;
 import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 
-import jalview.api.ComplexAlignFile;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GCutAndPasteTransfer;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
 /**
  * Cut'n'paste files into the desktop See JAL-1105
  * 
@@ -56,7 +59,9 @@ import jalview.util.MessageManager;
 public class CutAndPasteTransfer extends GCutAndPasteTransfer
 {
 
-  AlignViewport viewport;
+  AlignmentViewPanel alignpanel;
+
+  AlignViewportI viewport;
 
   FileParse source = null;
   public CutAndPasteTransfer()
@@ -74,9 +79,13 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   /**
    * DOCUMENT ME!
    */
-  public void setForInput(AlignViewport viewport)
+  public void setForInput(AlignmentViewPanel viewpanel)
   {
-    this.viewport = viewport;
+    this.alignpanel = viewpanel;
+    if (alignpanel != null)
+    {
+      this.viewport = alignpanel.getAlignViewport();
+    }
     if (viewport != null)
     {
       ok.setText(MessageManager.getString("action.add"));
@@ -186,15 +195,21 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
    */
   public void ok_actionPerformed(ActionEvent e)
   {
-    String format = new IdentifyFile().Identify(getText(), "Paste");
+    String text = getText();
+    if (text.trim().length() < 1)
+    {
+      return;
+    }
+
+    String format = new IdentifyFile().Identify(text, "Paste");
     // TODO: identify feature, annotation or tree file and parse appropriately.
-    Alignment al = null;
+    AlignmentI al = null;
 
     if (FormatAdapter.isValidFormat(format))
     {
       try
       {
-        FormatAdapter fa = new FormatAdapter(viewport);
+        FormatAdapter fa = new FormatAdapter(alignpanel);
         al = fa.readFile(getText(), "Paste", format);
         source = fa.getAlignFile();
 
@@ -216,7 +231,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
               { format });
       if (viewport != null)
       {
-        viewport.addAlignment(al, title);
+        ((AlignViewport) viewport).addAlignment(al, title);
       }
       else
       {
@@ -231,11 +246,13 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
           boolean showSeqFeatures = ((ComplexAlignFile) source)
                   .isShowSeqFeatures();
           ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+                  .getDisplayedFeatures();
           af = new AlignFrame(al, hiddenSeqs, colSel,
                   AlignFrame.DEFAULT_WIDTH,
                   AlignFrame.DEFAULT_HEIGHT);
-
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+          af.getViewport().setFeaturesDisplayed(fd);
           af.changeColour(cs);
         }
         else