X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=7b8ade66b621da54b43a9ba2756f47ebd214b59d;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=e18a5628293cbf1f58b80ad7c9b6a9d0453f1600;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java old mode 100755 new mode 100644 index e18a562..7b8ade6 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -1,34 +1,67 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.event.*; -import javax.swing.*; +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 jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; +import javax.swing.JMenuItem; +import javax.swing.JPopupMenu; +import javax.swing.SwingUtilities; /** - * DOCUMENT ME! + * Cut'n'paste files into the desktop See JAL-1105 * * @author $author$ * @version $Revision$ @@ -36,12 +69,17 @@ import jalview.jbgui.*; public class CutAndPasteTransfer extends GCutAndPasteTransfer { - AlignViewport viewport; + AlignmentViewPanel alignpanel; + + AlignViewportI viewport; + + AlignmentFileReaderI source = null; public CutAndPasteTransfer() { SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { textarea.requestFocus(); @@ -53,12 +91,16 @@ 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("Add"); + ok.setText(MessageManager.getString("action.add")); } getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH); @@ -78,7 +120,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * DOCUMENT ME! * * @param text - * DOCUMENT ME! + * DOCUMENT ME! */ public void setText(String text) { @@ -90,15 +132,17 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer textarea.append(text); } + @Override public void save_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY")); + 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"); + chooser.setDialogTitle( + MessageManager.getString("label.save_text_to_file")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -106,8 +150,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer { try { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(chooser.getSelectedFile())); + PrintWriter out = new PrintWriter( + new FileWriter(chooser.getSelectedFile())); out.print(getText()); out.close(); @@ -123,8 +167,9 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void copyItem_actionPerformed(ActionEvent e) { textarea.getSelectedText(); @@ -136,8 +181,9 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void pasteMenu_actionPerformed(ActionEvent e) { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); @@ -150,8 +196,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer try { - textarea.append((String) contents - .getTransferData(DataFlavor.stringFlavor)); + textarea.append( + (String) contents.getTransferData(DataFlavor.stringFlavor)); } catch (Exception ex) { } @@ -161,64 +207,153 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void ok_actionPerformed(ActionEvent e) { - String format = new IdentifyFile().Identify(getText(), "Paste"); - Alignment al = null; + String text = getText(); + if (text.trim().length() < 1) + { + return; + } - if (FormatAdapter.isValidFormat(format)) + FileFormatI format = null; + try { - try - { - al = new FormatAdapter().readFile(getText(), "Paste", format); - } catch (java.io.IOException ex) + 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()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Couldn't read the pasted text.\n" + ex.toString(), - "Error parsing text", JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + AppletFormatAdapter.getSupportedFormats(), + MessageManager.getString("label.couldnt_read_data"), + JvOptionPane.WARNING_MESSAGE); } + return; } - if (al != null) + // TODO: identify feature, annotation or tree file and parse appropriately. + AlignmentI al = null; + + try { - if (viewport != null) + 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) { - for (int i = 0; i < al.getHeight(); i++) + if (proxyColourScheme != null) { - viewport.getAlignment().addSequence(al.getSequenceAt(i)); + viewport.applyFeaturesStyle(proxyColourScheme); } - - 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) + { + 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); + 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, "Cut & Paste input - " + format, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - af.statusBar.setText("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 { - af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", - false)); + 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()) + { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + AppletFormatAdapter.getSupportedFormats(), + MessageManager.getString("label.couldnt_read_data"), + JvOptionPane.WARNING_MESSAGE); + } + } } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void cancel_actionPerformed(ActionEvent e) { try @@ -229,23 +364,32 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer } } + @Override public void textarea_mousePressed(MouseEvent e) { - if (SwingUtilities.isRightMouseButton(e)) + /* + * isPopupTrigger is checked in mousePressed on Mac, + * in mouseReleased on Windows + */ + if (e.isPopupTrigger()) { - JPopupMenu popup = new JPopupMenu("Edit"); - JMenuItem item = new JMenuItem("Copy"); + 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("Paste"); + item = new JMenuItem(MessageManager.getString("action.paste")); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pasteMenu_actionPerformed(e);