package eu.isas.peptideshaker.gui.exportdialogs;
import com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX;
import eu.isas.peptideshaker.followup.InclusionListExport;
import eu.isas.peptideshaker.followup.InclusionListExport.ExportFormat;
import eu.isas.peptideshaker.gui.PeptideShakerGUI;
import java.awt.Toolkit;
import java.io.File;
import java.util.ArrayList;
import javax.swing.JFileChooser;
import javax.swing.JOptionPane;
import javax.swing.filechooser.FileFilter;
/**
* Dialog for setting the inclusion list export settings.
*
* @author Harald Barsnes
* @author Marc Vaudel
*/
public class InclusionListExportDialog extends javax.swing.JDialog {
/**
* References to the follow up export dialog.
*/
private FollowupPreferencesDialog followupPreferencesDialog;
/**
* A simple progress dialog.
*/
private static ProgressDialogX progressDialog;
/**
* The export format.
*/
private ExportFormat exportFormat;
/**
* Creates a new InclusionListExportDialog.
*
* @param followupPreferencesDialog
* @param exportFormat
* @param modal
*/
public InclusionListExportDialog(FollowupPreferencesDialog followupPreferencesDialog, ExportFormat exportFormat, boolean modal) {
super(followupPreferencesDialog, modal);
this.followupPreferencesDialog = followupPreferencesDialog;
this.exportFormat = exportFormat;
initComponents();
setLocationRelativeTo(followupPreferencesDialog);
setVisible(true);
}
/**
* This method is called from within the constructor to initialize the form.
* WARNING: Do NOT modify this code. The content of this method is always
* regenerated by the Form Editor.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
backgroundPanel = new javax.swing.JPanel();
proteinFilterPanel = new javax.swing.JPanel();
relatedProteinsCheck = new javax.swing.JCheckBox();
relatredAndUnrelatedCheck = new javax.swing.JCheckBox();
unrelatedCheck = new javax.swing.JCheckBox();
peptideFilterPanel = new javax.swing.JPanel();
miscleavedCheck = new javax.swing.JCheckBox();
reactiveCheck = new javax.swing.JCheckBox();
degeneratedCheck = new javax.swing.JCheckBox();
rtFilterPanel = new javax.swing.JPanel();
rtWindow = new javax.swing.JTextField();
minRtWindowUnitLabel = new javax.swing.JLabel();
jLabel1 = new javax.swing.JLabel();
okButton = new javax.swing.JButton();
cancelButton = new javax.swing.JButton();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
setTitle("Export Settings");
setResizable(false);
backgroundPanel.setBackground(new java.awt.Color(230, 230, 230));
proteinFilterPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Protein Filter"));
proteinFilterPanel.setOpaque(false);
relatedProteinsCheck.setText("Related Proteins");
relatedProteinsCheck.setIconTextGap(15);
relatedProteinsCheck.setOpaque(false);
relatredAndUnrelatedCheck.setText("Related and Unrelated Proteins");
relatredAndUnrelatedCheck.setIconTextGap(15);
relatredAndUnrelatedCheck.setOpaque(false);
unrelatedCheck.setSelected(true);
unrelatedCheck.setText("Unrelated Proteins");
unrelatedCheck.setIconTextGap(15);
unrelatedCheck.setOpaque(false);
javax.swing.GroupLayout proteinFilterPanelLayout = new javax.swing.GroupLayout(proteinFilterPanel);
proteinFilterPanel.setLayout(proteinFilterPanelLayout);
proteinFilterPanelLayout.setHorizontalGroup(
proteinFilterPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(proteinFilterPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(proteinFilterPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(relatedProteinsCheck, javax.swing.GroupLayout.PREFERRED_SIZE, 169, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(relatredAndUnrelatedCheck)
.addComponent(unrelatedCheck))
.addContainerGap(37, Short.MAX_VALUE))
);
proteinFilterPanelLayout.setVerticalGroup(
proteinFilterPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(proteinFilterPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(relatedProteinsCheck)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(relatredAndUnrelatedCheck)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(unrelatedCheck)
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
peptideFilterPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Peptide Filter"));
peptideFilterPanel.setOpaque(false);
miscleavedCheck.setSelected(true);
miscleavedCheck.setText("Miscleaved Peptides");
miscleavedCheck.setIconTextGap(15);
miscleavedCheck.setOpaque(false);
reactiveCheck.setSelected(true);
reactiveCheck.setText("Reactive Peptides");
reactiveCheck.setIconTextGap(15);
reactiveCheck.setOpaque(false);
degeneratedCheck.setSelected(true);
degeneratedCheck.setText("Degenerated Peptides");
degeneratedCheck.setIconTextGap(15);
degeneratedCheck.setOpaque(false);
javax.swing.GroupLayout peptideFilterPanelLayout = new javax.swing.GroupLayout(peptideFilterPanel);
peptideFilterPanel.setLayout(peptideFilterPanelLayout);
peptideFilterPanelLayout.setHorizontalGroup(
peptideFilterPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(peptideFilterPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(peptideFilterPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(degeneratedCheck)
.addComponent(reactiveCheck)
.addComponent(miscleavedCheck, javax.swing.GroupLayout.PREFERRED_SIZE, 169, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
peptideFilterPanelLayout.setVerticalGroup(
peptideFilterPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(peptideFilterPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(miscleavedCheck)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(reactiveCheck)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(degeneratedCheck)
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
rtFilterPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Retention Time Filter"));
rtFilterPanel.setOpaque(false);
rtWindow.setHorizontalAlignment(javax.swing.JTextField.CENTER);
rtWindow.setText("20");
minRtWindowUnitLabel.setText("s");
jLabel1.setText("Min RT");
javax.swing.GroupLayout rtFilterPanelLayout = new javax.swing.GroupLayout(rtFilterPanel);
rtFilterPanel.setLayout(rtFilterPanelLayout);
rtFilterPanelLayout.setHorizontalGroup(
rtFilterPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(rtFilterPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(jLabel1)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(rtWindow)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(minRtWindowUnitLabel)
.addContainerGap())
);
rtFilterPanelLayout.setVerticalGroup(
rtFilterPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(rtFilterPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(rtFilterPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(rtWindow, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(minRtWindowUnitLabel)
.addComponent(jLabel1))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
okButton.setText("OK");
okButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
okButtonActionPerformed(evt);
}
});
cancelButton.setText("Cancel");
cancelButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cancelButtonActionPerformed(evt);
}
});
javax.swing.GroupLayout backgroundPanelLayout = new javax.swing.GroupLayout(backgroundPanel);
backgroundPanel.setLayout(backgroundPanelLayout);
backgroundPanelLayout.setHorizontalGroup(
backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(backgroundPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(peptideFilterPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(proteinFilterPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(rtFilterPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, backgroundPanelLayout.createSequentialGroup()
.addGap(0, 0, Short.MAX_VALUE)
.addComponent(okButton)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(cancelButton)))
.addContainerGap())
);
backgroundPanelLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {cancelButton, okButton});
backgroundPanelLayout.setVerticalGroup(
backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(backgroundPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(proteinFilterPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(peptideFilterPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(rtFilterPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(okButton)
.addComponent(cancelButton))
.addContainerGap())
);
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(backgroundPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(backgroundPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
);
pack();
}// </editor-fold>//GEN-END:initComponents
/**
* Close the dialog without exporting.
*
* @param evt
*/
private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
dispose();
}//GEN-LAST:event_cancelButtonActionPerformed
/**
* Open a file chooser and when file is selected start the export.
*
* @param evt
*/
private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
if (validateInput()) {
final JFileChooser fileChooser = new JFileChooser(followupPreferencesDialog.getPeptideShakerGUI().getLastSelectedFolder());
fileChooser.setDialogTitle("Select Destination File");
fileChooser.setMultiSelectionEnabled(false);
FileFilter filter = new FileFilter() {
@Override
public boolean accept(File myFile) {
return myFile.isDirectory() || myFile.getName().endsWith(exportFormat.extension);
}
@Override
public String getDescription() {
switch (exportFormat) {
case Thermo:
return "(Thermo inclusion list) .txt";
case ABI:
return "(ABI inclusion list) .txt";
case Bruker:
return "(Bruker inclusion list) .csv";
case MassLynx:
return "(MassLynx inclusion list) .txt";
default:
return "(unknown format) .txt";
}
}
};
fileChooser.setFileFilter(filter);
int returnVal = fileChooser.showSaveDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION) {
File tempOutputFile = fileChooser.getSelectedFile();
tempOutputFile = ExportFormat.verifyFileExtension(tempOutputFile, exportFormat);
int outcome = JOptionPane.YES_OPTION;
if (tempOutputFile.exists()) {
outcome = JOptionPane.showConfirmDialog(this,
"Should " + tempOutputFile + " be overwritten?", "Selected File Already Exists",
JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
}
if (outcome == JOptionPane.YES_OPTION) {
dispose();
progressDialog = new ProgressDialogX(this, followupPreferencesDialog.getPeptideShakerGUI(),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")),
true);
progressDialog.setPrimaryProgressCounterIndeterminate(true);
progressDialog.setTitle("Exporting. Please Wait...");
// needed due to threading issues
final File outputFile = tempOutputFile;
new Thread(new Runnable() {
public void run() {
progressDialog.setVisible(true);
}
}, "ProgressDialog").start();
new Thread("SaveThread") {
@Override
public void run() {
try {
PeptideShakerGUI peptideShakerGUI = followupPreferencesDialog.getPeptideShakerGUI();
InclusionListExport.exportInclusionList(outputFile, peptideShakerGUI.getIdentification(),
peptideShakerGUI.getIdentificationFeaturesGenerator(), getProteinFilters(), getPeptideFilters(),
exportFormat, peptideShakerGUI.getSearchParameters(), WIDTH, progressDialog, peptideShakerGUI.getFilterPreferences());
boolean processCancelled = progressDialog.isRunCanceled();
progressDialog.setRunFinished();
if (!processCancelled) {
JOptionPane.showMessageDialog(followupPreferencesDialog, "Inclusion list saved to " + fileChooser.getSelectedFile().getName() + ".",
"Save Complete", JOptionPane.INFORMATION_MESSAGE);
}
} catch (Exception e) {
progressDialog.setRunFinished();
e.printStackTrace();
JOptionPane.showMessageDialog(followupPreferencesDialog, "An error occurred when saving the file.", "Saving Failed", JOptionPane.ERROR_MESSAGE);
}
}
}.start();
}
}
}
}//GEN-LAST:event_okButtonActionPerformed
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JPanel backgroundPanel;
private javax.swing.JButton cancelButton;
private javax.swing.JCheckBox degeneratedCheck;
private javax.swing.JLabel jLabel1;
private javax.swing.JLabel minRtWindowUnitLabel;
private javax.swing.JCheckBox miscleavedCheck;
private javax.swing.JButton okButton;
private javax.swing.JPanel peptideFilterPanel;
private javax.swing.JPanel proteinFilterPanel;
private javax.swing.JCheckBox reactiveCheck;
private javax.swing.JCheckBox relatedProteinsCheck;
private javax.swing.JCheckBox relatredAndUnrelatedCheck;
private javax.swing.JPanel rtFilterPanel;
private javax.swing.JTextField rtWindow;
private javax.swing.JCheckBox unrelatedCheck;
// End of variables declaration//GEN-END:variables
/**
* Validates the user's input.
*
* @return a boolean indicating whether the input is valid.
*/
private boolean validateInput() {
try {
new Double(rtWindow.getText().trim());
} catch (Exception e) {
JOptionPane.showMessageDialog(this, "Please verify the input for the RT minimal window.", "Wrong input", JOptionPane.WARNING_MESSAGE);
return false;
}
return true;
}
/**
* Returns the protein filters selected as list of PI statuses.
*
* @return the protein filters
*/
private ArrayList<Integer> getProteinFilters() {
ArrayList<Integer> proteinFilters = new ArrayList<Integer>();
if (relatedProteinsCheck.isSelected()) {
proteinFilters.add(1);
}
if (relatredAndUnrelatedCheck.isSelected()) {
proteinFilters.add(2);
}
if (unrelatedCheck.isSelected()) {
proteinFilters.add(3);
}
return proteinFilters;
}
/**
* Returns the peptide filters selected as a list of PeptideFilterType.
*
* @return the peptide filters
*/
private ArrayList<InclusionListExport.PeptideFilterType> getPeptideFilters() {
ArrayList<InclusionListExport.PeptideFilterType> peptideFilters = new ArrayList<InclusionListExport.PeptideFilterType>();
if (miscleavedCheck.isSelected()) {
peptideFilters.add(InclusionListExport.PeptideFilterType.miscleaved);
}
if (degeneratedCheck.isSelected()) {
peptideFilters.add(InclusionListExport.PeptideFilterType.degenerated);
}
if (reactiveCheck.isSelected()) {
peptideFilters.add(InclusionListExport.PeptideFilterType.reactive);
}
return peptideFilters;
}
}