X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=112d502d9abb2335cbece27b241f1229f947cf74;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=10f97777baeeac135d82b5257cd0de86591bf0c6;hpb=64a0d836635dc75e58f93f730c490ed2ce9ffaef;p=jalview.git diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java old mode 100755 new mode 100644 index 10f9777..112d502 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -1,178 +1,404 @@ -/* - * 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.*; -import javax.swing.event.InternalFrameEvent; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class CutAndPasteTransfer extends GCutAndPasteTransfer -{ - /** - * DOCUMENT ME! - */ - public void setForInput() - { - getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH); - SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - textarea.requestFocus(); - } - }); - } - - /** - * 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); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void copyItem_actionPerformed(ActionEvent e) - { - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - c.setContents(new StringSelection(textarea.getText()), 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.setText((String) contents.getTransferData( - DataFlavor.stringFlavor)); - } - catch (Exception ex) - { - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void ok_actionPerformed(ActionEvent e) - { - String format = IdentifyFile.Identify(getText(), "Paste"); - SequenceI[] sequences = null; - - if (FormatAdapter.formats.contains(format)) - { - sequences = FormatAdapter.readFile(getText(), "Paste", format); - } - - if (sequences != 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( jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); - } - catch (Exception ex) - { - } - - try - { - this.setClosed(true); - } - 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); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void cancel_actionPerformed(ActionEvent e) - { - try - { - this.setClosed(true); - } - catch (Exception ex) - { - } - } -} +/* + * 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 . + * 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); + + } + } + +}