JAL-1760 JAL-1641 Serialisation of Hidden Seqs and Cols in JSON output. Added ability...

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 0ebb952..6f15ddf 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,16 +20,31 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
+import jalview.datamodel.Alignment;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.HtmlFile;
+import jalview.io.IdentifyFile;
+import jalview.io.JSONFile;
+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;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+
 /**
  * Cut'n'paste files into the desktop See JAL-1105
  * 
@@ -41,6 +56,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
   AlignViewport viewport;
 
+  FileParse source = null;
   public CutAndPasteTransfer()
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -176,7 +192,10 @@ 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,
@@ -190,28 +209,33 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
     if (al != null)
     {
+      String title = MessageManager.formatMessage(
+              "label.input_cut_paste_params", new String[]
+              { format });
       if (viewport != null)
       {
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-          viewport.getAlignment().addSequence(al.getSequenceAt(i));
-        }
-
-        viewport.firePropertyChange("alignment", null, viewport
-                .getAlignment().getSequences());
+        viewport.addAlignment(al, title);
       }
       else
       {
         AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
         af.currentFileFormat = format;
-        Desktop.addInternalFrame(af, MessageManager.formatMessage(
-                "label.input_cut_paste_params", new String[]
-                { format }), AlignFrame.DEFAULT_WIDTH,
+        Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
         af.statusBar.setText(MessageManager
                 .getString("label.successfully_pasted_alignment_file"));
 
+        if (source instanceof HtmlFile)
+        {
+          ((HtmlFile) source).applySettingsToAlignmentView(af);
+        }
+        else if (source instanceof JSONFile)
+        {
+          ((JSONFile) source).applySettingsToAlignmentView(af);
+        }
+
+
         try
         {
           af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
@@ -223,6 +247,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     }
   }
 
+
   /**
    * DOCUMENT ME!
    *