X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=3da42fc6af8ebf686796afe44489459865039827;hb=42ed2d813b3b8e7c9c80d79e1c8e1ded61ec6dd9;hp=a10f43304f1bbb23e9684b1267eab5b4bd5fced3;hpb=3cc7159787bd31859f7bc27916e7ff854b895280;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index a10f433..3da42fc 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -40,6 +40,8 @@ import javax.swing.*;
 public class CutAndPasteTransfer extends GCutAndPasteTransfer
 {
 
+  AlignViewport viewport;
+
   public CutAndPasteTransfer()
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -55,9 +57,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     /**
      * DOCUMENT ME!
      */
-    public void setForInput()
+    public void setForInput(AlignViewport viewport)
     {
-        getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
+      this.viewport = viewport;
+      getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
     }
 
     /**
@@ -80,6 +83,45 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         textarea.setText(text);
     }
 
+    public void appendText(String text)
+    {
+      textarea.append(text);
+    }
+
+
+    public void save_actionPerformed(ActionEvent e)
+    {
+      JalviewFileChooser chooser = new JalviewFileChooser(
+          jalview.bin.Cache.getProperty(
+              "LAST_DIRECTORY"));
+
+      chooser.setAcceptAllFileFilterUsed(false);
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle("Save Text to File");
+      chooser.setToolTipText("Save");
+
+      int value = chooser.showSaveDialog(this);
+
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        try
+        {
+          java.io.PrintWriter out = new java.io.PrintWriter(
+              new java.io.FileWriter(chooser.getSelectedFile()));
+
+          out.print(getText());
+          out.close();
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+
+      }
+    }
+
+
+
     /**
      * DOCUMENT ME!
      *
@@ -124,45 +166,53 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
      */
     public void ok_actionPerformed(ActionEvent e)
     {
-        String format = IdentifyFile.Identify(getText(), "Paste");
+        String format = new IdentifyFile().Identify(getText(), "Paste");
         SequenceI[] sequences = null;
 
         if (FormatAdapter.formats.contains(format))
         {
+          try{
             sequences = new FormatAdapter().readFile(getText(), "Paste", format);
+          }catch(java.io.IOException ex)
+          {
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                  "Couldn't read the pasted text.\n" +ex.toString(),
+                                                  "Error parsing text",
+                                                  JOptionPane.WARNING_MESSAGE);
+          }
         }
 
         if (sequences != null)
         {
+          if(viewport!=null)
+          {
+            for(int i=0; i<sequences.length; i++)
+              viewport.getAlignment().addSequence(sequences[i]);
+
+            viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+          }
+          else
+          {
             AlignFrame af = new AlignFrame(new Alignment(sequences));
             af.currentFileFormat = format;
             Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
-                AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+                                     AlignFrame.NEW_WINDOW_WIDTH,
+                                     AlignFrame.NEW_WINDOW_HEIGHT);
             af.statusBar.setText("Successfully pasted alignment file");
 
-            try
-            {
-                af.setMaximum( jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
-            }
-            catch (Exception ex)
+            if(jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
             {
+              af.wrapMenuItem.setSelected(true);
+              af.wrapMenuItem_actionPerformed(null);
             }
-
             try
             {
-                this.setClosed(true);
+              af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
             }
             catch (Exception ex)
             {
             }
-        }
-        else
-        {
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                "Couldn't read the pasted text.\n" +
-                "Formats currently supported are\n" +
-                "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",
-                "Error parsing text", JOptionPane.WARNING_MESSAGE);
+          }
         }
     }
 
@@ -203,7 +253,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
                   }
             });
         popup.add(item);
-        popup.show(this, e.getX(), e.getY()+textarea.getY()+30);
+        popup.show(this, e.getX()+10, e.getY()+textarea.getY()+40);
 
       }
     }