X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=5e3650079533ddf0cb6bd73ea78930d0ec0de767;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=f608a524d21ef21f2f6dca6e70209a24a4f49c64;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
old mode 100755
new mode 100644
index f608a52..5e36500
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,33 +1,68 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 .
+ * 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 java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import javax.swing.*;
+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 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 $Revision$
@@ -35,12 +70,17 @@ 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();
@@ -52,12 +92,16 @@ 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);
@@ -89,15 +133,19 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
textarea.append(text);
}
+ @Override
public void save_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 JalviewFileChooser - Save option
+
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ 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);
@@ -105,8 +153,8 @@ 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();
@@ -124,6 +172,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
* @param e
* DOCUMENT ME!
*/
+ @Override
public void copyItem_actionPerformed(ActionEvent e)
{
textarea.getSelectedText();
@@ -137,6 +186,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pasteMenu_actionPerformed(ActionEvent e)
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -149,8 +199,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
try
{
- textarea.append((String) contents
- .getTransferData(DataFlavor.stringFlavor));
+ textarea.append(
+ (String) contents.getTransferData(DataFlavor.stringFlavor));
} catch (Exception ex)
{
}
@@ -162,55 +212,140 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
* @param e
* DOCUMENT ME!
*/
+ @Override
public void ok_actionPerformed(ActionEvent e)
{
- String format = new IdentifyFile().Identify(getText(), "Paste");
- // TODO: identify feature, annotation or tree file and parse appropriately.
- 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)
- {
- for (int i = 0; i < al.getHeight(); i++)
- {
- viewport.getAlignment().addSequence(al.getSequenceAt(i));
- }
+ 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);
+ }
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ 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 = 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);
+ 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, "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.setStatus(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
- false));
+ 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);
+ }
+ }
}
/**
@@ -219,6 +354,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
* @param e
* DOCUMENT ME!
*/
+ @Override
public void cancel_actionPerformed(ActionEvent e)
{
try
@@ -229,23 +365,32 @@ 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);