JAL-1443 data validation for empty content before loading alignment from file or...

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

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 77d8fc7..979d1aa 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 2.8.2)
- * 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 +20,36 @@
  */
 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.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;
+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
  * 
@@ -39,8 +59,11 @@ import jalview.util.MessageManager;
 public class CutAndPasteTransfer extends GCutAndPasteTransfer
 {
 
-  AlignViewport viewport;
+  AlignmentViewPanel alignpanel;
 
+  AlignViewportI viewport;
+
+  FileParse source = null;
   public CutAndPasteTransfer()
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -56,9 +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"));
@@ -100,7 +127,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
     chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Text to File");
+    chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -168,43 +195,77 @@ 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
       {
-        al = new FormatAdapter().readFile(getText(), "Paste", format);
+        FormatAdapter fa = new FormatAdapter(alignpanel);
+        al = fa.readFile(getText(), "Paste", format);
+        source = fa.getAlignFile();
+
       } catch (java.io.IOException ex)
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                       MessageManager.formatMessage("label.couldnt_read_pasted_text", new String[]{ex.toString()}),
-                MessageManager.getString("label.error_parsing_text"), JOptionPane.WARNING_MESSAGE);
+                MessageManager.formatMessage(
+                        "label.couldnt_read_pasted_text", new String[]
+                        { ex.toString() }), MessageManager
+                        .getString("label.error_parsing_text"),
+                JOptionPane.WARNING_MESSAGE);
       }
     }
 
     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());
+        ((AlignViewport) viewport).addAlignment(al, title);
       }
       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();
+          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
+        {
+          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, AlignFrame.DEFAULT_HEIGHT);
-        af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
+        Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
+        af.statusBar.setText(MessageManager
+                .getString("label.successfully_pasted_alignment_file"));
 
         try
         {
@@ -217,6 +278,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     }
   }
 
+
   /**
    * DOCUMENT ME!
    * 
@@ -237,8 +299,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   {
     if (SwingUtilities.isRightMouseButton(e))
     {
-      JPopupMenu popup = new JPopupMenu(MessageManager.getString("action.edit"));
-      JMenuItem item = new JMenuItem(MessageManager.getString("action.copy"));
+      JPopupMenu popup = new JPopupMenu(
+              MessageManager.getString("action.edit"));
+      JMenuItem item = new JMenuItem(
+              MessageManager.getString("action.copy"));
       item.addActionListener(new ActionListener()
       {
         public void actionPerformed(ActionEvent e)