-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
+/*
+ * 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.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.api.FeaturesSourceI;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+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 java.awt.*;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
+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.datatransfer.*;
-import jalview.datamodel.Alignment;
-import jalview.io.FormatAdapter;
-import jalview.datamodel.SequenceI;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
-import jalview.io.IdentifyFile;
+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
{
- public void setForInput()
+
+ AlignmentViewPanel alignpanel;
+
+ AlignViewportI viewport;
+
+ FileParse source = null;
+
+ public CutAndPasteTransfer()
{
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ 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);
+ }
+
+ @Override
+ 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!
+ */
+ @Override
public void copyItem_actionPerformed(ActionEvent e)
{
+ textarea.getSelectedText();
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- c.setContents( new StringSelection( textarea.getText()) , null ) ;
+ c.setContents(new StringSelection(textarea.getSelectedText()), null);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
public void pasteMenu_actionPerformed(ActionEvent e)
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
Transferable contents = c.getContents(this);
+
if (contents == null)
+ {
return;
- try{
- textarea.setText( (String) contents.getTransferData(DataFlavor.
- stringFlavor));
- }catch(Exception ex){}
+ }
+
+ try
+ {
+ textarea.append((String) contents
+ .getTransferData(DataFlavor.stringFlavor));
+ } catch (Exception ex)
+ {
+ }
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
public void ok_actionPerformed(ActionEvent e)
{
- String format = IdentifyFile.Identify(getText(), "Paste");
- SequenceI [] sequences = null;
+ String text = getText();
+ if (text.trim().length() < 1)
+ {
+ return;
+ }
+
+ String format = new IdentifyFile().identify(text, "Paste");
+ if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+ {
+ System.err.println(MessageManager
+ .getString("label.couldnt_read_data"));
+ if (!Jalview.isHeadlessMode())
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.SUPPORTED_FORMATS,
+ MessageManager.getString("label.couldnt_read_data"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ return;
+ }
+
+ // TODO: identify feature, annotation or tree file and parse appropriately.
+ AlignmentI al = null;
- if (FormatAdapter.formats.contains( format ))
- sequences = FormatAdapter.readFile(getText(), "Paste", format);
+ 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(sequences!=null)
+ if (al != null && al.hasValidSequence())
+ {
+ String title = MessageManager.formatMessage(
+ "label.input_cut_paste_params", new String[] { format });
+ FeatureSettingsModelI proxyColourScheme = source
+ .getFeatureColourScheme();
+
+ /*
+ * if the view panel was closed its alignment is nulled
+ * and this is an orphaned cut and paste window
+ */
+ if (viewport != null && viewport.getAlignment() != null)
+ {
+ if (proxyColourScheme != null)
{
- 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");
- try
- { af.setMaximum(Preferences.showFullscreen); }
- catch (Exception ex)
- {}
- try
+ viewport.applyFeaturesStyle(proxyColourScheme);
+ }
+ ((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();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ 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);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
{
- this.setClosed(true);
+ af.changeColour(cs);
}
- 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);
+ {
+ af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (source instanceof FeaturesSourceI)
+ {
+ af.getViewport().setShowSequenceFeatures(true);
+ }
+ }
+ if (proxyColourScheme != null)
+ {
+ af.getViewport().applyFeaturesStyle(proxyColourScheme);
+ }
+ 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)
+ {
+ }
+ }
+ }
+ else
+ {
+ System.err.println(MessageManager
+ .getString("label.couldnt_read_data"));
+ if (!Jalview.isHeadlessMode())
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.SUPPORTED_FORMATS,
+ MessageManager.getString("label.couldnt_read_data"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
public void cancel_actionPerformed(ActionEvent e)
{
- try{
+ try
+ {
this.setClosed(true);
- }catch(Exception ex){}
+ } catch (Exception ex)
+ {
+ }
}
+ @Override
+ public void textarea_mousePressed(MouseEvent e)
+ {
+ /*
+ * isPopupTrigger is checked in mousePressed on Mac,
+ * in mouseReleased on Windows
+ */
+ if (e.isPopupTrigger())
+ {
+ JPopupMenu popup = new JPopupMenu(
+ MessageManager.getString("action.edit"));
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("action.copy"));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ copyItem_actionPerformed(e);
+ }
+ });
+ popup.add(item);
+ item = new JMenuItem(MessageManager.getString("action.paste"));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteMenu_actionPerformed(e);
+ }
+ });
+ popup.add(item);
+ popup.show(this, e.getX() + 10, e.getY() + textarea.getY() + 40);
+
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff