JAL-1780 JAL-653 organise imports

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 22f0a59..f3c4d87 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -20,14 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.Alignment;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GCutAndPasteTransfer;
-import jalview.util.MessageManager;
-
 import java.awt.Toolkit;
 import java.awt.datatransfer.Clipboard;
 import java.awt.datatransfer.DataFlavor;
@@ -42,6 +34,19 @@ 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
  * 
@@ -53,6 +58,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
   AlignViewport viewport;
 
+  FileParse source = null;
   public CutAndPasteTransfer()
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -188,7 +194,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     {
       try
       {
-        al = new FormatAdapter().readFile(getText(), "Paste", format);
+        FormatAdapter fa = new FormatAdapter(viewport);
+        al = fa.readFile(getText(), "Paste", format);
+        source = fa.getAlignFile();
+
       } catch (java.io.IOException ex)
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -211,8 +220,30 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
       }
       else
       {
-        AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-                AlignFrame.DEFAULT_HEIGHT);
+
+        AlignFrame af;
+        if (source instanceof ComplexAlignFile)
+        {
+          ColumnSelection colSel = ((ComplexAlignFile) source)
+                  .getColumnSelection();
+          SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+                  .getHiddenSequences();
+          boolean showSeqFeatures = ((ComplexAlignFile) source)
+                  .isShowSeqFeatures();
+          ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          af = new AlignFrame(al, hiddenSeqs, colSel,
+                  AlignFrame.DEFAULT_WIDTH,
+                  AlignFrame.DEFAULT_HEIGHT);
+
+          af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+          af.changeColour(cs);
+        }
+        else
+        {
+          af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+                  AlignFrame.DEFAULT_HEIGHT);
+        }
+
         af.currentFileFormat = format;
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
@@ -230,6 +261,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     }
   }
 
+
   /**
    * DOCUMENT ME!
    *