Multiple Views

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index f2920e5..b857405 100755 (executable)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -29,7 +29,6 @@ import java.awt.datatransfer.*;
 import java.awt.event.*;\r
 \r
 import javax.swing.*;\r
-import javax.swing.event.InternalFrameEvent;\r
 \r
 \r
 /**\r
@@ -40,19 +39,28 @@ import javax.swing.event.InternalFrameEvent;
  */\r
 public class CutAndPasteTransfer extends GCutAndPasteTransfer\r
 {\r
+\r
+  AlignViewport viewport;\r
+\r
+  public CutAndPasteTransfer()\r
+  {\r
+    SwingUtilities.invokeLater(new Runnable()\r
+    {\r
+      public void run()\r
+      {\r
+        textarea.requestFocus();\r
+      }\r
+    });\r
+\r
+  }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      */\r
-    public void setForInput()\r
+    public void setForInput(AlignViewport viewport)\r
     {\r
-        getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);\r
-          SwingUtilities.invokeLater(new Runnable()\r
-          {\r
-            public void run()\r
-            {\r
-              textarea.requestFocus();\r
-            }\r
-          });\r
+      this.viewport = viewport;\r
+      getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);\r
     }\r
 \r
     /**\r
@@ -75,6 +83,45 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         textarea.setText(text);\r
     }\r
 \r
+    public void appendText(String text)\r
+    {\r
+      textarea.append(text);\r
+    }\r
+\r
+\r
+    public void save_actionPerformed(ActionEvent e)\r
+    {\r
+      JalviewFileChooser chooser = new JalviewFileChooser(\r
+          jalview.bin.Cache.getProperty(\r
+              "LAST_DIRECTORY"));\r
+\r
+      chooser.setAcceptAllFileFilterUsed(false);\r
+      chooser.setFileView(new JalviewFileView());\r
+      chooser.setDialogTitle("Save Text to File");\r
+      chooser.setToolTipText("Save");\r
+\r
+      int value = chooser.showSaveDialog(this);\r
+\r
+      if (value == JalviewFileChooser.APPROVE_OPTION)\r
+      {\r
+        try\r
+        {\r
+          java.io.PrintWriter out = new java.io.PrintWriter(\r
+              new java.io.FileWriter(chooser.getSelectedFile()));\r
+\r
+          out.print(getText());\r
+          out.close();\r
+        }\r
+        catch (Exception ex)\r
+        {\r
+          ex.printStackTrace();\r
+        }\r
+\r
+      }\r
+    }\r
+\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -82,8 +129,9 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
      */\r
     public void copyItem_actionPerformed(ActionEvent e)\r
     {\r
+        textarea.getSelectedText();\r
         Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
-        c.setContents(new StringSelection(textarea.getText()), null);\r
+        c.setContents(new StringSelection(textarea.getSelectedText()), null);\r
     }\r
 \r
     /**\r
@@ -118,45 +166,50 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
      */\r
     public void ok_actionPerformed(ActionEvent e)\r
     {\r
-        String format = IdentifyFile.Identify(getText(), "Paste");\r
+        String format = new IdentifyFile().Identify(getText(), "Paste");\r
         SequenceI[] sequences = null;\r
 \r
-        if (FormatAdapter.formats.contains(format))\r
+        if (FormatAdapter.isValidFormat(format))\r
         {\r
+          try{\r
             sequences = new FormatAdapter().readFile(getText(), "Paste", format);\r
+          }catch(java.io.IOException ex)\r
+          {\r
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                                                  "Couldn't read the pasted text.\n" +ex.toString(),\r
+                                                  "Error parsing text",\r
+                                                  JOptionPane.WARNING_MESSAGE);\r
+          }\r
         }\r
 \r
         if (sequences != null)\r
         {\r
-            AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+          if(viewport!=null)\r
+          {\r
+            for(int i=0; i<sequences.length; i++)\r
+              viewport.getAlignment().addSequence(sequences[i]);\r
+\r
+            viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+          }\r
+          else\r
+          {\r
+            AlignFrame af = new AlignFrame(new Alignment(sequences),\r
+                                           AlignFrame.DEFAULT_WIDTH,\r
+                                           AlignFrame.DEFAULT_HEIGHT);\r
             af.currentFileFormat = format;\r
             Desktop.addInternalFrame(af, "Cut & Paste input - " + format,\r
-                AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
+                                     AlignFrame.DEFAULT_WIDTH,\r
+                                     AlignFrame.DEFAULT_HEIGHT);\r
             af.statusBar.setText("Successfully pasted alignment file");\r
 \r
             try\r
             {\r
-                af.setMaximum( jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
+              af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
             }\r
             catch (Exception ex)\r
             {\r
             }\r
-\r
-            try\r
-            {\r
-                this.setClosed(true);\r
-            }\r
-            catch (Exception ex)\r
-            {\r
-            }\r
-        }\r
-        else\r
-        {\r
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-                "Couldn't read the pasted text.\n" +\r
-                "Formats currently supported are\n" +\r
-                "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",\r
-                "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
+          }\r
         }\r
     }\r
 \r
@@ -197,7 +250,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
                   }\r
             });\r
         popup.add(item);\r
-        popup.show(this, e.getX(), e.getY()+30);\r
+        popup.show(this, e.getX()+10, e.getY()+textarea.getY()+40);\r
 \r
       }\r
     }\r