X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=979d1aa0f4b274e2a286028d34efd292918e714f;hb=58399507cc82e8c7940a8500af73c3ed1bdd720d;hp=3da42fc6af8ebf686796afe44489459865039827;hpb=2140ff9720fb75b29d13bd48350eda2808cb05f9;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
old mode 100755
new mode 100644
index 3da42fc..979d1aa
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,261 +1,328 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class CutAndPasteTransfer extends GCutAndPasteTransfer
-{
-
-  AlignViewport viewport;
-
-  public CutAndPasteTransfer()
-  {
-    SwingUtilities.invokeLater(new Runnable()
-    {
-      public void run()
-      {
-        textarea.requestFocus();
-      }
-    });
-
-  }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void setForInput(AlignViewport viewport)
-    {
-      this.viewport = viewport;
-      getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getText()
-    {
-        return textarea.getText();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param text DOCUMENT ME!
-     */
-    public void setText(String text)
-    {
-        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!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void copyItem_actionPerformed(ActionEvent e)
-    {
-        textarea.getSelectedText();
-        Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-        c.setContents(new StringSelection(textarea.getSelectedText()), null);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void pasteMenu_actionPerformed(ActionEvent e)
-    {
-        Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-        Transferable contents = c.getContents(this);
-
-        if (contents == null)
-        {
-            return;
-        }
-
-        try
-        {
-            textarea.append((String) contents.getTransferData(
-                    DataFlavor.stringFlavor));
-        }
-        catch (Exception ex)
-        {
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void ok_actionPerformed(ActionEvent e)
-    {
-        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);
-            af.statusBar.setText("Successfully pasted alignment file");
-
-            if(jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
-            {
-              af.wrapMenuItem.setSelected(true);
-              af.wrapMenuItem_actionPerformed(null);
-            }
-            try
-            {
-              af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
-            }
-            catch (Exception ex)
-            {
-            }
-          }
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void cancel_actionPerformed(ActionEvent e)
-    {
-        try
-        {
-            this.setClosed(true);
-        }
-        catch (Exception ex)
-        {
-        }
-    }
-
-    public void textarea_mousePressed(MouseEvent e)
-    {
-      if(SwingUtilities.isRightMouseButton(e))
-      {
-        JPopupMenu popup = new JPopupMenu("Edit");
-        JMenuItem item = new JMenuItem("Copy");
-        item.addActionListener(new ActionListener()
-            {public void actionPerformed(ActionEvent e)
-                  {
-                    copyItem_actionPerformed(e);
-                  }
-            });
-        popup.add(item);
-        item = new JMenuItem("Paste");
-        item.addActionListener(new ActionListener()
-            {public void actionPerformed(ActionEvent e)
-                  {
-                    pasteMenu_actionPerformed(e);
-                  }
-            });
-        popup.add(item);
-        popup.show(this, e.getX()+10, e.getY()+textarea.getY()+40);
-
-      }
-    }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+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
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class CutAndPasteTransfer extends GCutAndPasteTransfer
+{
+
+  AlignmentViewPanel alignpanel;
+
+  AlignViewportI viewport;
+
+  FileParse source = null;
+  public CutAndPasteTransfer()
+  {
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        textarea.requestFocus();
+      }
+    });
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void setForInput(AlignmentViewPanel viewpanel)
+  {
+    this.alignpanel = viewpanel;
+    if (alignpanel != null)
+    {
+      this.viewport = alignpanel.getAlignViewport();
+    }
+    if (viewport != null)
+    {
+      ok.setText(MessageManager.getString("action.add"));
+    }
+
+    getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String getText()
+  {
+    return textarea.getText();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param text
+   *          DOCUMENT ME!
+   */
+  public void setText(String text)
+  {
+    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(MessageManager.getString("label.save_text_to_file"));
+    chooser.setToolTipText(MessageManager.getString("action.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!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void copyItem_actionPerformed(ActionEvent e)
+  {
+    textarea.getSelectedText();
+    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    c.setContents(new StringSelection(textarea.getSelectedText()), null);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void pasteMenu_actionPerformed(ActionEvent e)
+  {
+    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    Transferable contents = c.getContents(this);
+
+    if (contents == null)
+    {
+      return;
+    }
+
+    try
+    {
+      textarea.append((String) contents
+              .getTransferData(DataFlavor.stringFlavor));
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    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.
+    AlignmentI al = null;
+
+    if (FormatAdapter.isValidFormat(format))
+    {
+      try
+      {
+        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);
+      }
+    }
+
+    if (al != null)
+    {
+      String title = MessageManager.formatMessage(
+              "label.input_cut_paste_params", new String[]
+              { format });
+      if (viewport != null)
+      {
+        ((AlignViewport) viewport).addAlignment(al, title);
+      }
+      else
+      {
+
+        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, title, AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
+        af.statusBar.setText(MessageManager
+                .getString("label.successfully_pasted_alignment_file"));
+
+        try
+        {
+          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+                  false));
+        } catch (Exception ex)
+        {
+        }
+      }
+    }
+  }
+
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      this.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  public void textarea_mousePressed(MouseEvent e)
+  {
+    if (SwingUtilities.isRightMouseButton(e))
+    {
+      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)
+        {
+          copyItem_actionPerformed(e);
+        }
+      });
+      popup.add(item);
+      item = new JMenuItem(MessageManager.getString("action.paste"));
+      item.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          pasteMenu_actionPerformed(e);
+        }
+      });
+      popup.add(item);
+      popup.show(this, e.getX() + 10, e.getY() + textarea.getY() + 40);
+
+    }
+  }
+
+}