/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* 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 .
*/
package jalview.gui;
import java.util.*;
import java.util.List;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
import jalview.datamodel.*;
import jalview.io.*;
/**
*
* GUI dialog for exporting features or alignment annotations depending upon
* which method is called.
*
* @author AMW
*
*/
public class AnnotationExporter extends JPanel
{
JInternalFrame frame;
AlignmentPanel ap;
boolean features = true;
AlignmentAnnotation[] annotations;
List sequenceGroups;
Hashtable alignmentProperties;
public AnnotationExporter()
{
try
{
jbInit();
} catch (Exception ex)
{
ex.printStackTrace();
}
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
frame.getPreferredSize().height);
}
public void exportFeatures(AlignmentPanel ap)
{
this.ap = ap;
features = true;
CSVFormat.setVisible(false);
frame.setTitle("Export Features");
}
public void exportAnnotations(AlignmentPanel ap,
AlignmentAnnotation[] annotations, List list,
Hashtable alProperties)
{
this.ap = ap;
features = false;
GFFFormat.setVisible(false);
CSVFormat.setVisible(true);
this.annotations = annotations;
this.sequenceGroups = list;
this.alignmentProperties = alProperties;
frame.setTitle("Export Annotations");
}
public void toFile_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(features ? "Save Features to File"
: "Save Annotation to File");
chooser.setToolTipText("Save");
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String text = "No features found on alignment";
if (features)
{
if (GFFFormat.isSelected())
{
text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
.getDataset().getSequencesArray(),
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
}
else
{
text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
.getDataset().getSequencesArray(),
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
}
}
else
{
if (CSVFormat.isSelected())
{
text = new AnnotationFile().printCSVAnnotations(annotations);
}
else
{
text = new AnnotationFile().printAnnotations(annotations,
sequenceGroups, alignmentProperties);
}
}
try
{
java.io.PrintWriter out = new java.io.PrintWriter(
new java.io.FileWriter(chooser.getSelectedFile()));
out.print(text);
out.close();
} catch (Exception ex)
{
ex.printStackTrace();
}
}
close_actionPerformed(null);
}
public void toTextbox_actionPerformed(ActionEvent e)
{
String text = "No features found on alignment";
if (features)
{
if (GFFFormat.isSelected())
{
text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
.getDataset().getSequencesArray(),
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
}
else
{
text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
.getDataset().getSequencesArray(),
getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
}
}
else if (!features)
{
if (CSVFormat.isSelected())
{
text = new AnnotationFile().printCSVAnnotations(annotations);
}
else
{
text = new AnnotationFile().printAnnotations(annotations,
sequenceGroups, alignmentProperties);
}
}
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
cap.setText(text);
Desktop.addInternalFrame(cap, (features ? "Features for - "
: "Annotations for - ") + ap.alignFrame.getTitle(), 600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("generating "
+ (features ? "Features for - " : "Annotations for - ")
+ ap.alignFrame.getTitle(), oom);
cap.dispose();
}
close_actionPerformed(null);
}
private Hashtable getDisplayedFeatureCols()
{
Hashtable fcols = new Hashtable();
if (ap.av.featuresDisplayed == null)
{
return fcols;
}
Enumeration en = ap.av.featuresDisplayed.keys();
FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
// higher
// level
// method ?
while (en.hasMoreElements())
{
Object col = en.nextElement();
fcols.put(col, fr.featureColours.get(col));
}
return fcols;
}
public void close_actionPerformed(ActionEvent e)
{
try
{
frame.setClosed(true);
} catch (java.beans.PropertyVetoException ex)
{
}
}
private void jbInit() throws Exception
{
this.setLayout(new BorderLayout());
toFile.setText("to File");
toFile.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
toFile_actionPerformed(e);
}
});
toTextbox.setText("to Textbox");
toTextbox.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
toTextbox_actionPerformed(e);
}
});
close.setText("Close");
close.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
close_actionPerformed(e);
}
});
jalviewFormat.setOpaque(false);
jalviewFormat.setSelected(true);
jalviewFormat.setText("Jalview");
GFFFormat.setOpaque(false);
GFFFormat.setText("GFF");
CSVFormat.setOpaque(false);
CSVFormat.setText("CSV(Spreadsheet)");
jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
jLabel1.setText("Format: ");
this.setBackground(Color.white);
jPanel3.setBorder(BorderFactory.createEtchedBorder());
jPanel3.setOpaque(false);
jPanel1.setOpaque(false);
jPanel1.add(toFile);
jPanel1.add(toTextbox);
jPanel1.add(close);
jPanel3.add(jLabel1);
jPanel3.add(jalviewFormat);
jPanel3.add(GFFFormat);
jPanel3.add(CSVFormat);
buttonGroup.add(jalviewFormat);
buttonGroup.add(GFFFormat);
buttonGroup.add(CSVFormat);
this.add(jPanel3, BorderLayout.CENTER);
this.add(jPanel1, BorderLayout.SOUTH);
}
JPanel jPanel1 = new JPanel();
JButton toFile = new JButton();
JButton toTextbox = new JButton();
JButton close = new JButton();
ButtonGroup buttonGroup = new ButtonGroup();
JRadioButton jalviewFormat = new JRadioButton();
JRadioButton GFFFormat = new JRadioButton();
JRadioButton CSVFormat = new JRadioButton();
JLabel jLabel1 = new JLabel();
JPanel jPanel3 = new JPanel();
FlowLayout flowLayout1 = new FlowLayout();
}