package PDVGUI.gui.utils.FileImport;
import PDVGUI.gui.*;
import com.compomics.util.experiment.biology.PTMFactory;
import com.compomics.util.experiment.identification.identification_parameters.PtmSettings;
import com.compomics.util.experiment.identification.identification_parameters.SearchParameters;
import com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings;
import com.compomics.util.experiment.massspectrometry.SpectrumFactory;
import com.compomics.util.gui.GuiUtilities;
import com.compomics.util.gui.renderers.AlignedListCellRenderer;
import com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX;
import org.apache.commons.io.FileUtils;
import javax.swing.*;
import javax.swing.border.TitledBorder;
import javax.swing.filechooser.FileFilter;
import java.awt.*;
import java.awt.event.*;
import java.io.File;
import java.util.ArrayList;
import java.util.Objects;
/**
* Selecting de novo identification file and spectrum file, then putting them into DB
* Created by Ken on 2016/11/11.
*/
public class DeNovoImportDialog extends JDialog {
private JLabel idFileLabel;
private JLabel spectrumFileLabel;
private JTextField idFileJTextField;
private JTextField spectrumFileJTextField;
private JButton startJButton;
private JComboBox precursorIonUnit;
private JLabel fragmentIonLbl;
private JTextField fragmentIonAccuracyTxt;
/**
* Identification file
*/
private File identificationFile;
/**
* Spectrum file
*/
private File spectrumFile;
/**
* welcome dialog parent, can be null
*/
private PDVStart pdvStart;
/**
* Old frame to restart
*/
private JFrame oldJFrame;
/**
* LastSelectedFolder for opening easily
*/
private String lastSelectedFolder;
/**
* MS2 ion tolerance
*/
private Double fragmentIonMZTolerance = 0.05;
/**
* MS2 ion tolerance type (ppm or dal)
*/
private PDVMainClass.MassAccuracyType fragmentAccuracyType;
/**
* PTMFactory import from utilities
*/
private PTMFactory ptmFactory = PTMFactory.getInstance();
/**
* Parent class
*/
private PDVMainClass pdvMainClass;
/**
* New open dialog
* @param pdvStart welcome dialog parent frame
* @param pdvMainClass pdvMainClass
*/
public DeNovoImportDialog(PDVStart pdvStart, PDVMainClass pdvMainClass) {
super(pdvStart, true);
this.pdvStart = pdvStart;
this.pdvMainClass = pdvMainClass;
setUpGui();
setIconImage(Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")));
this.setLocationRelativeTo(pdvStart);
setVisible(true);
}
/**
* New open dialog
* @param pdvMainClass pdvMainClass dialog parent frame
* @param modal boolean
*/
public DeNovoImportDialog(PDVMainClass pdvMainClass, boolean modal, JFrame oldJFrame) {
super(pdvMainClass, modal);
this.pdvMainClass = pdvMainClass;
this.pdvStart = null;
this.oldJFrame = oldJFrame;
setUpGui();
setIconImage(Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")));
this.setLocationRelativeTo(pdvMainClass);
setVisible(true);
}
/**
* New open dialog.
* @param singlePeptideDisplay singlePeptideDisplay dialog parent frame
* @param modal boolean
*/
public DeNovoImportDialog(SinglePeptideDisplay singlePeptideDisplay, boolean modal, JFrame oldJFrame) {
super(singlePeptideDisplay, modal);
this.pdvStart = null;
this.oldJFrame = oldJFrame;
setUpGui();
setIconImage(Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")));
this.setLocationRelativeTo(pdvStart);
setVisible(true);
}
/**
* Set up the GUI
*/
private void setUpGui() {
initComponents();
idFileJTextField.setText("No file selected");
spectrumFileJTextField.setText("No file selected");
fragmentIonAccuracyTxt.setText("0.05");
precursorIonUnit.setEnabled(true);
precursorIonUnit.setRenderer(new AlignedListCellRenderer(0));
validateInput();
GuiUtilities.installEscapeCloseOperation(this);
}
/**
* Init all GUI components
*/
private void initComponents() {
startJButton = new JButton();
idFileLabel = new JLabel();
spectrumFileLabel = new JLabel();
idFileJTextField = new JTextField();
spectrumFileJTextField = new JTextField();
precursorIonUnit = new JComboBox();
fragmentIonLbl = new JLabel();
fragmentIonAccuracyTxt = new JTextField();
JPanel inputJPanel = new JPanel();
JPanel annotationSettingJPanel = new JPanel();
JPanel mainJPanel = new JPanel();
JButton browseIdJButton = new JButton();
JButton browseSpectraJButton = new JButton();
setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
setTitle("PDV - DeNovo Result Display");
setResizable(false);
addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent evt) {
formWindowClosing(evt);
}
});
mainJPanel.setBackground(new Color(250, 250, 250));
startJButton.setBackground(Color.green);
startJButton.setFont(new Font("Lucida", Font.BOLD, 13));
startJButton.setText("Start");
startJButton.setEnabled(false);
startJButton.setOpaque(false);
startJButton.addActionListener(this::startJButtonActionPerformed);
TitledBorder titledBorder = BorderFactory.createTitledBorder("Input Files" + " \t ");
titledBorder.setTitleFont(new Font("Console", Font.PLAIN, 12));
inputJPanel.setBorder(titledBorder);
inputJPanel.setOpaque(false);
idFileLabel.setForeground(new Color(255, 0, 0));
idFileLabel.setFont(new Font("Arial", Font.PLAIN, 12));
idFileLabel.setText("Identification File *");
idFileJTextField.setEditable(false);
idFileJTextField.setBackground(Color.WHITE);
idFileJTextField.setOpaque(false);
idFileJTextField.setHorizontalAlignment(JTextField.CENTER);
browseIdJButton.setIcon(new ImageIcon(getClass().getResource("/icons/open.png")));
browseIdJButton.setBorder(null);
browseIdJButton.setBorderPainted(false);
browseIdJButton.setContentAreaFilled(false);
browseIdJButton.addActionListener(this::browseIdJButtonActionPerformed);
spectrumFileLabel.setForeground(new Color(255, 0, 0));
spectrumFileLabel.setFont(new Font("Arial", Font.PLAIN, 12));
spectrumFileLabel.setText("Spectrum File *");
spectrumFileJTextField.setEditable(false);
spectrumFileJTextField.setBackground(Color.WHITE);
spectrumFileJTextField.setOpaque(false);
spectrumFileJTextField.setHorizontalAlignment(JTextField.CENTER);
browseSpectraJButton.setIcon(new ImageIcon(getClass().getResource("/icons/open.png")));
browseSpectraJButton.setBorder(null);
browseSpectraJButton.setBorderPainted(false);
browseSpectraJButton.setContentAreaFilled(false);
browseSpectraJButton.addActionListener(this::browseSpectraJButtonActionPerformed);
titledBorder = BorderFactory.createTitledBorder("Project Settings" + " \t ");
titledBorder.setTitleFont(new Font("Console", Font.PLAIN, 12));
annotationSettingJPanel.setBorder(titledBorder);
annotationSettingJPanel.setOpaque(false);
precursorIonUnit.setModel(new DefaultComboBoxModel(new String[]{"Da", "ppm"}));
precursorIonUnit.setBackground(Color.WHITE);
precursorIonUnit.setOpaque(false);
fragmentIonLbl.setText("Fragment m/z Tolerance");
fragmentIonLbl.setFont(new Font("Arial", Font.PLAIN, 12));
fragmentIonAccuracyTxt.setHorizontalAlignment(0);
fragmentIonAccuracyTxt.addKeyListener(new KeyAdapter() {
public void keyReleased(KeyEvent evt) {
fragmentIonAccuracyTxtKeyReleased(evt);
}
});
GroupLayout annotationSettingJPanelLayout = new GroupLayout(annotationSettingJPanel);
annotationSettingJPanel.setLayout(annotationSettingJPanelLayout);
annotationSettingJPanelLayout.setHorizontalGroup(
annotationSettingJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(annotationSettingJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(annotationSettingJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(annotationSettingJPanelLayout.createSequentialGroup()
.addComponent(fragmentIonLbl,GroupLayout.PREFERRED_SIZE, 220, GroupLayout.PREFERRED_SIZE)
.addComponent(fragmentIonAccuracyTxt,GroupLayout.PREFERRED_SIZE, 50, GroupLayout.PREFERRED_SIZE)
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(precursorIonUnit,GroupLayout.PREFERRED_SIZE, 70, GroupLayout.PREFERRED_SIZE))
)
.addContainerGap())
);
annotationSettingJPanelLayout.setVerticalGroup(
annotationSettingJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(annotationSettingJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(annotationSettingJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(fragmentIonLbl)
.addComponent(fragmentIonAccuracyTxt)
.addComponent(precursorIonUnit))
)
);
GroupLayout inputFilesPanelLayout = new GroupLayout(inputJPanel);
inputJPanel.setLayout(inputFilesPanelLayout);
inputFilesPanelLayout.setHorizontalGroup(
inputFilesPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(inputFilesPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(inputFilesPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(GroupLayout.Alignment.TRAILING, inputFilesPanelLayout.createSequentialGroup()
.addComponent(idFileLabel, GroupLayout.PREFERRED_SIZE, 160, GroupLayout.PREFERRED_SIZE)
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
.addComponent(idFileJTextField,GroupLayout.PREFERRED_SIZE,260, GroupLayout.PREFERRED_SIZE)
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(browseIdJButton))
.addGroup(inputFilesPanelLayout.createSequentialGroup()
.addComponent(spectrumFileLabel, GroupLayout.PREFERRED_SIZE, 160, GroupLayout.PREFERRED_SIZE)
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
.addComponent(spectrumFileJTextField,GroupLayout.PREFERRED_SIZE, 260, GroupLayout.PREFERRED_SIZE)
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(browseSpectraJButton)))
.addContainerGap())
);
inputFilesPanelLayout.linkSize(SwingConstants.HORIZONTAL, new Component[] {browseIdJButton});
inputFilesPanelLayout.linkSize(SwingConstants.HORIZONTAL, new Component[] {browseSpectraJButton});
inputFilesPanelLayout.setVerticalGroup(
inputFilesPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(inputFilesPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(inputFilesPanelLayout.createParallelGroup(GroupLayout.Alignment.BASELINE)
.addComponent(idFileJTextField, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
.addComponent(idFileLabel)
.addComponent(browseIdJButton))
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
.addGroup(inputFilesPanelLayout.createParallelGroup(GroupLayout.Alignment.BASELINE)
.addComponent(spectrumFileLabel)
.addComponent(browseSpectraJButton)
.addComponent(spectrumFileJTextField, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE))
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
.addContainerGap(GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
GroupLayout mainJPanelLayout = new GroupLayout(mainJPanel);
mainJPanel.setLayout(mainJPanelLayout);
mainJPanelLayout.setHorizontalGroup(
mainJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(mainJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(mainJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(mainJPanelLayout.createSequentialGroup()
.addGap(150, 220, 730)
.addComponent(startJButton, GroupLayout.PREFERRED_SIZE, 100, GroupLayout.PREFERRED_SIZE)
.addGap(15, 15, 15))
.addComponent(inputJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(annotationSettingJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
)
.addContainerGap())
);
mainJPanelLayout.setVerticalGroup(
mainJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(mainJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(inputJPanel, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(annotationSettingJPanel, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED)
.addGroup(mainJPanelLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addComponent(startJButton, GroupLayout.PREFERRED_SIZE, 30, GroupLayout.PREFERRED_SIZE))
.addContainerGap())
);
GroupLayout layout = new GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(mainJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
layout.setVerticalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(mainJPanel, GroupLayout.PREFERRED_SIZE, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE)
);
pack();
}
/**
* Closes the dialog
* @param evt Window click event
*/
private void formWindowClosing(WindowEvent evt) {
this.dispose();
}
/**
* Import all files and open new De novo frame
* @param evt mouse click event
*/
private void startJButtonActionPerformed(ActionEvent evt) {
if (pdvStart != null) {
pdvStart.setVisible(false);
}
if(oldJFrame != null){
oldJFrame.setVisible(false);
}
this.setVisible(false);
pdvMainClass.setVisible(true);
ProgressDialogX progressDialog = new ProgressDialogX(pdvMainClass,
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMassWait.png")),
true);
progressDialog.setPrimaryProgressCounterIndeterminate(true);
progressDialog.setTitle("Loading Data. Please Wait...");
new Thread(() -> {
try {
progressDialog.setVisible(true);
} catch (IndexOutOfBoundsException e) {
}
}, "ProgressDialog").start();
new Thread("SetUp") {
@Override
public void run() {
ArrayList<String> modification = ptmFactory.getPTMs();
PtmSettings ptmSettings = new PtmSettings();
for(String fixedModification:modification){
ptmSettings.addFixedModification(ptmFactory.getPTM(fixedModification));
}
for(String variableModification:modification){
ptmSettings.addVariableModification(ptmFactory.getPTM(variableModification));
}
SearchParameters searchParameters = new SearchParameters();
searchParameters.setPtmSettings(ptmSettings);
if(precursorIonUnit.getSelectedIndex() == 0){
searchParameters.setFragmentAccuracyType(SearchParameters.MassAccuracyType.DA);
}else {
searchParameters.setFragmentAccuracyType(SearchParameters.MassAccuracyType.PPM);
}
searchParameters.setFragmentIonAccuracy(fragmentIonMZTolerance);
AnnotationSettings annotationPreferences = new AnnotationSettings();
annotationPreferences.setPreferencesFromSearchParameters(searchParameters);
annotationPreferences.setFragmentIonAccuracy(fragmentIonMZTolerance);
pdvMainClass.setAnnotationSettings(annotationPreferences);
pdvMainClass.setSearchParameters(searchParameters);
if(precursorIonUnit.getSelectedIndex() == 0){
fragmentAccuracyType = PDVMainClass.MassAccuracyType.DA;
}else {
fragmentAccuracyType = PDVMainClass.MassAccuracyType.PPM;
}
pdvMainClass.setFragmentAccuracyType(fragmentAccuracyType);
if (identificationFile != null) {
SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
try {
if (spectrumFile.getName().endsWith(".dup")){
if (new File(spectrumFile.getAbsolutePath()+".mgf").exists()){
spectrumFile = new File(spectrumFile.getAbsolutePath()+".mgf");
} else {
FileUtils.copyFile(spectrumFile, new File(spectrumFile.getAbsolutePath()+".mgf"));
spectrumFile = new File(spectrumFile.getAbsolutePath()+".mgf");
}
}
spectrumFactory.addSpectra(spectrumFile);
} catch (Exception e) {
JOptionPane.showMessageDialog(DeNovoImportDialog.this, "Failed to pares Spectrum file. Please check your spectrum file!", "File Error", JOptionPane.WARNING_MESSAGE);
progressDialog.setRunFinished();
e.printStackTrace();
System.exit(1);
}
progressDialog.setRunFinished();
if (identificationFile.getName().endsWith(".tab")){
pdvMainClass.importDeepNovoResults(identificationFile, spectrumFile, spectrumFactory);
} else if (identificationFile.getName().endsWith(".tsk")){
pdvMainClass.importPNovoResults(identificationFile, spectrumFile, spectrumFactory);
} else {
pdvMainClass.importDeNovoResults(identificationFile, spectrumFile, spectrumFactory);
}
}
}
}.start();
}
/**
* fragmentIonAccuracyTxtKeyReleased
* @param evt key event
*/
private void fragmentIonAccuracyTxtKeyReleased(KeyEvent evt) {
if(!Objects.equals(fragmentIonAccuracyTxt.getText(), "") && fragmentIonAccuracyTxt.getText() != null){
fragmentIonMZTolerance = Double.valueOf(fragmentIonAccuracyTxt.getText());
} else {
fragmentIonMZTolerance = null;
}
validateInput();
}
/**
* Validates input information and enable start button
*/
private void validateInput() {
boolean allValid = true;
if (identificationFile != null) {
idFileLabel.setForeground(Color.BLACK);
idFileLabel.setToolTipText(null);
} else {
idFileLabel.setForeground(Color.RED);
idFileLabel.setToolTipText("Please select identification file");
idFileJTextField.setToolTipText("Please select identification file");
idFileJTextField.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
allValid = false;
}
if (spectrumFile != null) {
spectrumFileLabel.setForeground(Color.BLACK);
spectrumFileLabel.setToolTipText(null);
} else {
spectrumFileLabel.setForeground(Color.RED);
spectrumFileLabel.setToolTipText("Please select the spectrum file for the identification file");
spectrumFileJTextField.setToolTipText("Please select the spectrum file for the identification file");
spectrumFileJTextField.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
allValid = false;
}
if (fragmentIonMZTolerance != null) {
fragmentIonLbl.setForeground(Color.BLACK);
fragmentIonLbl.setToolTipText(null);
} else {
fragmentIonLbl.setForeground(Color.RED);
fragmentIonLbl.setToolTipText("Please input MS2 ion tolerance!");
allValid = false;
}
startJButton.setEnabled(allValid);
}
/**
* Import identification file
* @param evt mouse click event
*/
private void browseIdJButtonActionPerformed(ActionEvent evt) {
JFileChooser fileChooser = new JFileChooser(lastSelectedFolder);
fileChooser.setDialogTitle("Select Identification File");
fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
fileChooser.setMultiSelectionEnabled(true);
FileFilter filter = new FileFilter() {
@Override
public boolean accept(File myFile) {
return myFile.getName().toLowerCase().endsWith(".tags")
|| myFile.getName().toLowerCase().endsWith("novor.csv")
|| myFile.getName().toLowerCase().endsWith(".out")
|| myFile.getName().toLowerCase().endsWith(".tab")
|| myFile.getName().toLowerCase().endsWith(".tsk")
|| myFile.isDirectory();
}
@Override
public String getDescription() {
return " pepNovo+ (.out), DirecTag (.tags), DeepNovo (.tab), pNovo (.tsk) and Novor (.novor.csv)";
}
};
fileChooser.setFileFilter(filter);
int returnValue = fileChooser.showDialog(this, "OK");
if (returnValue == JFileChooser.APPROVE_OPTION) {
File selectedFile = fileChooser.getSelectedFile();
if (selectedFile != null) {
lastSelectedFolder = selectedFile.getParent();
identificationFile = selectedFile;
idFileJTextField.setText(identificationFile.getName() + " selected");
validateInput();
}
}
}
/**
* Import spectrum file
* @param evt mouse click event
*/
private void browseSpectraJButtonActionPerformed(ActionEvent evt) {
JFileChooser fileChooser = new JFileChooser(lastSelectedFolder);
fileChooser.setDialogTitle("Select Spectrum File");
fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
fileChooser.setMultiSelectionEnabled(true);
FileFilter filter = new FileFilter() {
@Override
public boolean accept(File myFile) {
return myFile.getName().toLowerCase().endsWith(".mgf")
|| myFile.getName().toLowerCase().endsWith(".dup")
|| myFile.isDirectory();
}
@Override
public String getDescription() {
return " Mascot Generic Format (.mgf)";
}
};
fileChooser.setFileFilter(filter);
int returnValue = fileChooser.showDialog(this, "OK");
if (returnValue == JFileChooser.APPROVE_OPTION) {
File[] selectedFiles = fileChooser.getSelectedFiles();
for (File selectedFile : selectedFiles) {
if (selectedFile.exists()) {
spectrumFile = selectedFile;
lastSelectedFolder = selectedFile.getParent();
}
}
spectrumFileJTextField.setText(spectrumFile.getName() + " selected.");
validateInput();
}
}
}
