-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import java.awt.datatransfer.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.jbgui.*;\r
-\r
-public class CutAndPasteTransfer\r
- extends GCutAndPasteTransfer\r
-{\r
- public void setForInput()\r
- {\r
- getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);\r
- }\r
-\r
- public String getText()\r
- {\r
- return textarea.getText();\r
- }\r
-\r
- public void setText(String text)\r
- {\r
- textarea.setText(text);\r
- }\r
-\r
- public void copyItem_actionPerformed(ActionEvent e)\r
- {\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- c.setContents(new StringSelection(textarea.getText()), null);\r
- }\r
-\r
- public void pasteMenu_actionPerformed(ActionEvent e)\r
- {\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- Transferable contents = c.getContents(this);\r
-\r
- if (contents == null)\r
- {\r
- return;\r
- }\r
-\r
- try\r
- {\r
- textarea.setText( (String) contents.getTransferData(\r
- DataFlavor.stringFlavor));\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
- String format = IdentifyFile.Identify(getText(), "Paste");\r
- SequenceI[] sequences = null;\r
-\r
- if (FormatAdapter.formats.contains(format))\r
- {\r
- sequences = FormatAdapter.readFile(getText(), "Paste", format);\r
- }\r
-\r
- if (sequences != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- af.currentFileFormat = format;\r
- Desktop.addInternalFrame(af, "Cut & Paste input - " + format,\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
-\r
- try\r
- {\r
- af.setMaximum(Preferences.showFullscreen);\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",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
- }\r
-\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- this.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-}\r
+/*
+ * 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.bin.Cache;
+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.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentFileReaderI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteTransfer;
+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.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+
+import javax.swing.JMenuItem;
+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;
+
+ AlignmentFileReaderI 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)
+ {
+ // TODO: JAL-3048 JalviewFileChooser - Save option
+
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ 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
+ {
+ PrintWriter out = new PrintWriter(
+ new 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.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.append(
+ (String) contents.getTransferData(DataFlavor.stringFlavor));
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ String text = getText();
+ if (text.trim().length() < 1)
+ {
+ return;
+ }
+
+ FileFormatI format = null;
+ try
+ {
+ format = new IdentifyFile().identify(text, DataSourceType.PASTE);
+ } catch (FileFormatException e1)
+ {
+ // leave as null
+ }
+ if (format == null)
+ {
+ System.err
+ .println(MessageManager.getString("label.couldnt_read_data"));
+ if (!Jalview.isHeadlessMode())
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.getSupportedFormats(),
+ MessageManager.getString("label.couldnt_read_data"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ return;
+ }
+
+ // TODO: identify feature, annotation or tree file and parse appropriately.
+ AlignmentI al = null;
+
+ try
+ {
+ FormatAdapter fa = new FormatAdapter(alignpanel);
+ al = fa.readFile(getText(), DataSourceType.PASTE, format);
+ source = fa.getAlignFile();
+
+ } catch (IOException ex)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.couldnt_read_pasted_text", new String[]
+ { ex.toString() }),
+ MessageManager.getString("label.error_parsing_text"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+
+ if (al != null && al.hasValidSequence())
+ {
+ String title = MessageManager
+ .formatMessage("label.input_cut_paste_params", new String[]
+ { format.getName() });
+ 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)
+ {
+ ((AlignViewport) viewport).addAlignment(al, title);
+ viewport.applyFeaturesStyle(proxyColourScheme);
+ }
+ else
+ {
+
+ AlignFrame af;
+ if (source instanceof ComplexAlignFile)
+ {
+ HiddenColumns hidden = ((ComplexAlignFile) source)
+ .getHiddenColumns();
+ 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, hidden,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+ af.getViewport().setFeaturesDisplayed(fd);
+ af.setMenusForViewport();
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
+ }
+ else
+ {
+ 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.setStatus(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
+
+ try
+ {
+ af.setMaximum(
+ Cache.getDefault("SHOW_FULLSCREEN", false));
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ else
+ {
+ System.err
+ .println(MessageManager.getString("label.couldnt_read_data"));
+ if (!Jalview.isHeadlessMode())
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.getSupportedFormats(),
+ MessageManager.getString("label.couldnt_read_data"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ this.setClosed(true);
+ } 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