package PDVGUI.gui;
import PDVGUI.gui.utils.*;
import PDVGUI.gui.utils.FileImport.DatabaseImportDialog;
import PDVGUI.gui.utils.FileImport.DeNovoImportDialog;
import com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler;
import com.compomics.util.experiment.biology.*;
import com.compomics.util.experiment.identification.identification_parameters.PtmSettings;
import com.compomics.util.experiment.identification.identification_parameters.SearchParameters;
import com.compomics.util.experiment.identification.matches.ModificationMatch;
import com.compomics.util.experiment.identification.matches.SpectrumMatch;
import com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings;
import com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption;
import com.compomics.util.experiment.massspectrometry.*;
import com.compomics.util.gui.JOptionEditorPane;
import com.compomics.util.gui.filehandling.TempFilesManager;
import com.compomics.util.gui.renderers.AlignedListCellRenderer;
import com.compomics.util.gui.spectrum.SpectrumPanel;
import com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX;
import com.compomics.util.preferences.DigestionPreferences;
import com.compomics.util.preferences.LastSelectedFolder;
import com.compomics.util.preferences.UtilitiesUserPreferences;
import org.json.JSONArray;
import uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException;
import javax.swing.*;
import javax.swing.border.TitledBorder;
import javax.swing.filechooser.FileFilter;
import java.awt.*;
import java.awt.event.*;
import java.io.*;
import java.net.MalformedURLException;
import java.net.ProtocolException;
import java.util.*;
import java.net.HttpURLConnection;
import java.net.URL;
import org.json.JSONObject;
/**
* Single peptide check
* Created by Ken on 7/5/2017.
*/
public class SinglePeptideDisplay extends JFrame {
private File spectrumFile;
private String peptideSequence;
private MSnSpectrum currentSpectrum;
private PeptideAssumption peptideAssumption;
private JPanel inputJPanel;
private JPanel spectrumJPanel;
private JPanel peptideSequenceJPanel;
private JScrollPane peptideSequenceJScrollPane;
private JLabel spectrumFileJLabel;
private JComboBox spectrumSourceBox;
private JLabel peptideSequenceJLabel;
private JTextField spectrumFileJText;
private JButton spectrumFileJButton;
private JTextField usiIDJText;
private JButton getUSIJButton;
private JTextField peptideSequenceJText;
private JButton startJButton;
private JPanel spectrumAnnotationMenuPanel;
private JPanel spectrumShowJPanel;
private JMenuBar annotationMenuBar;
private JMenu switchPaneMenu;
private JComboBox precursorIonUnit;
private JTextField fragmentIonAccuracyTxt;
/**
* Progress dialog
*/
private ProgressDialogX progressDialog;
/**
* ExceptionHandler import from utilities
*/
private FrameExceptionHandler exceptionHandler = new FrameExceptionHandler(this, "https://github.com/wenbostar/PDV");
/**
* PTMFactory import from utilities
*/
private PTMFactory ptmFactory = PTMFactory.getInstance();
/**
* Annotation settings
*/
private AnnotationSettings annotationSettings = new AnnotationSettings();
/**
* Sequencing parameters
*/
public SearchParameters searchParameters;
/**
* Utilities user preferences
*/
public UtilitiesUserPreferences utilitiesUserPreferences;
/**
* All modifications map
*/
private HashMap<String, ArrayList<String>> aASingleModification;
/**
* peptide Modifications
*/
private ArrayList<ModificationMatch> modificationMatches = new ArrayList<>();
/**
* All modifications sites map
*/
private ArrayList<Integer> indexOfModification = new ArrayList<>();
/**
* Button list
*/
private ArrayList<JButton> allButtons;
/**
* Last selected folder
*/
public LastSelectedFolder lastSelectedFolder = new LastSelectedFolder();
/**
* Spectrum main Panel
*/
private SpectrumMainPanel spectrumMainPanel;
/**
* Main constructor
*/
public SinglePeptideDisplay(){
try {
utilitiesUserPreferences = UtilitiesUserPreferences.loadUserPreferences();
} catch (Exception e) {
e.printStackTrace();
}
annotationSettings.setIntensityLimit(0.3);
setUpGUI();
setExtendedState(MAXIMIZED_BOTH);
this.setVisible(true);
aASingleModification = getModification();
}
/**
* Set up GUI
*/
private void setUpGUI(){
spectrumMainPanel = new SpectrumMainPanel(this);
initComponents();
fragmentIonAccuracyTxt.setText("0.05");
spectrumAnnotationMenuPanel.add(annotationMenuBar);
this.precursorIonUnit.setEnabled(true);
this.precursorIonUnit.setRenderer(new AlignedListCellRenderer(0));
this.spectrumSourceBox.setEnabled(true);
this.spectrumSourceBox.setRenderer(new AlignedListCellRenderer(0));
}
/**
* Init all GUI components
*/
private void initComponents(){
inputJPanel = new JPanel();
peptideSequenceJPanel = new JPanel();
peptideSequenceJScrollPane = new JScrollPane();
spectrumAnnotationMenuPanel = new JPanel();
spectrumJPanel = new JPanel();
spectrumShowJPanel = new JPanel();
spectrumFileJLabel = new JLabel();
peptideSequenceJLabel = new JLabel();
spectrumFileJText = new JTextField();
peptideSequenceJText = new JTextField();
startJButton = new JButton();
usiIDJText = new JTextField();
getUSIJButton = new JButton();
precursorIonUnit = new JComboBox();
spectrumSourceBox = new JComboBox();
fragmentIonAccuracyTxt = new JTextField();
annotationMenuBar = new JMenuBar();
switchPaneMenu = new JMenu();
JPanel mainJPanel = new JPanel();
JToolBar allJToolBar = new JToolBar();
spectrumFileJButton = new JButton();
JLabel fragmentIonLbl = new JLabel();
JMenuBar menuBar = new JMenuBar();
JMenu fileJMenu = new JMenu();
JMenuItem newJMenuItem = new JMenuItem();
JMenuItem openDenovoJMenuItem = new JMenuItem();
JMenuItem exitJMenuItem = new JMenuItem();
setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
setTitle("PDV - One PSM");
setBackground(new java.awt.Color(255, 255, 255));
setMinimumSize(new java.awt.Dimension(760, 600));
addWindowListener(new WindowAdapter() {
public void windowClosing(WindowEvent evt) {
formWindowClosing(evt);
}
});
setIconImage(Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")));
mainJPanel.setBackground(new java.awt.Color(255, 255, 255));
mainJPanel.setPreferredSize(new java.awt.Dimension(1260, 800));
menuBar.setBackground(new java.awt.Color(255, 255, 255));
fileJMenu.setMnemonic('F');
fileJMenu.setText("File");
newJMenuItem.setMnemonic('N');
newJMenuItem.setText("Open Database Result");
newJMenuItem.addActionListener(this::newJMenuItemActionPerformed);
//fileJMenu.add(newJMenuItem);
openDenovoJMenuItem.setMnemonic('D');
openDenovoJMenuItem.setText("Open DeNovo Result");
openDenovoJMenuItem.addActionListener(this::openDenovoJMenuItemActionPerformed);
//fileJMenu.add(openDenovoJMenuItem);
exitJMenuItem.setMnemonic('E');
exitJMenuItem.setText("Exist");
exitJMenuItem.addActionListener(this::exitJMenuItemActionPerformed);
fileJMenu.add(exitJMenuItem);
menuBar.add(fileJMenu);
setJMenuBar(menuBar);
TitledBorder titledBorder = BorderFactory.createTitledBorder("Input File and Peptide" + " \t ");
titledBorder.setTitleFont(new Font("Console", Font.PLAIN, 12));
inputJPanel.setBorder(titledBorder);
inputJPanel.setOpaque(false);
inputJPanel.setBackground(Color.white);
spectrumFileJLabel.setText("Spectrum File *");
spectrumFileJLabel.setFont(new Font("Console", Font.PLAIN, 12));
spectrumFileJLabel.setForeground(new Color(255, 0, 0));
spectrumSourceBox.setModel(new DefaultComboBoxModel(new String[]{"MGF", "USI"}));
spectrumSourceBox.addItemListener(this::spectrumSourceBoxMouseClicked);
spectrumFileJText.setEditable(false);
spectrumFileJText.setHorizontalAlignment(SwingConstants.CENTER);
spectrumFileJButton.setIcon(new ImageIcon(getClass().getResource("/icons/open.png")));
spectrumFileJButton.setBorder(null);
spectrumFileJButton.setBorderPainted(false);
spectrumFileJButton.setContentAreaFilled(false);
spectrumFileJButton.addActionListener(this::spectrumFileJButtonActionPerformed);
usiIDJText.setEditable(true);
usiIDJText.setHorizontalAlignment(SwingConstants.CENTER);
getUSIJButton.setIcon(new ImageIcon(getClass().getResource("/icons/search.png")));
getUSIJButton.setBorder(null);
getUSIJButton.setBorderPainted(false);
getUSIJButton.setContentAreaFilled(false);
getUSIJButton.addActionListener(this::getUSIJButtonActionPerformed);
peptideSequenceJLabel.setText("Peptide *");
peptideSequenceJLabel.setFont(new Font("Console", Font.PLAIN, 12));
peptideSequenceJLabel.setForeground(new Color(255, 0, 0));
peptideSequenceJText.setEditable(true);
peptideSequenceJText.setHorizontalAlignment(SwingConstants.CENTER);
peptideSequenceJText.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(KeyEvent evt) {
peptideSequenceJTextKeyReleased(evt);
}
});
startJButton.setText("Start");
startJButton.setBackground(Color.green);
startJButton.setEnabled(false);
startJButton.addActionListener(this::startJButtonActionPerformed);
precursorIonUnit.setModel(new DefaultComboBoxModel(new String[]{"Da", "ppm"}));
fragmentIonLbl.setText("Fragment m/z Tolerance");
fragmentIonLbl.setFont(new Font("Console", Font.PLAIN, 12));
fragmentIonAccuracyTxt.setHorizontalAlignment(0);
peptideSequenceJScrollPane.setVisible(false);
peptideSequenceJScrollPane.setToolTipText("Click the amino acid to select modification");
spectrumJPanel.setBackground(Color.white);
spectrumJPanel.setOpaque(false);
GroupLayout spectrumJPanelLayout = new GroupLayout(spectrumJPanel);
spectrumJPanel.setLayout(spectrumJPanelLayout);
spectrumJPanelLayout.setHorizontalGroup(
spectrumJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(spectrumJPanelLayout.createSequentialGroup()
.addComponent(spectrumFileJLabel, 150, 150, 150)
.addGap(30, 30, 30)
.addComponent(spectrumSourceBox, 90, 90, 90)
.addComponent(spectrumFileJText, GroupLayout.DEFAULT_SIZE, 280, 600)
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(spectrumFileJButton)
.addGap(20, 50, 100))
);
spectrumJPanelLayout.setVerticalGroup(
spectrumJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(spectrumJPanelLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addComponent(spectrumFileJLabel)
.addComponent(spectrumSourceBox, 20, 30 ,30)
.addComponent(spectrumFileJText, 20, 30 ,30)
.addComponent(spectrumFileJButton, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE, GroupLayout.PREFERRED_SIZE))
);
GroupLayout inputJPanelLayout = new GroupLayout(inputJPanel);
inputJPanel.setLayout(inputJPanelLayout);
inputJPanelLayout.setHorizontalGroup(
inputJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(inputJPanelLayout.createSequentialGroup()
.addGap(21,21,21)
.addComponent(spectrumJPanel)
.addGroup(inputJPanelLayout.createSequentialGroup()
.addComponent(peptideSequenceJLabel, 150, 150, 200)
.addComponent(peptideSequenceJText, GroupLayout.DEFAULT_SIZE, 150, 600))
.addGap(21,21,21))
.addComponent(peptideSequenceJScrollPane)
.addGroup(inputJPanelLayout.createSequentialGroup()
.addGap(21,21,21)
.addGroup(inputJPanelLayout.createSequentialGroup()
.addComponent(fragmentIonLbl, 150, 150, 150)
.addGap(30, 30, 30)
.addComponent(precursorIonUnit, 90, 90, 90)
//.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
.addComponent(fragmentIonAccuracyTxt, GroupLayout.DEFAULT_SIZE, 50, 70))
.addGap(10, 150, 500)
.addGap(20, 50, 200)
.addGroup(inputJPanelLayout.createParallelGroup(GroupLayout.Alignment.TRAILING)
.addGroup(inputJPanelLayout.createSequentialGroup()
.addGap(100,600,2000)
.addComponent(startJButton)))
.addGap(21,21,21))
);
//inputJPanelLayout.linkSize(SwingConstants.HORIZONTAL, new java.awt.Component[] {spectrumFileJLabel, fragmentIonLbl, peptideSequenceJLabel});
inputJPanelLayout.setVerticalGroup(
inputJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(inputJPanelLayout.createSequentialGroup()
.addGap(15,15,15)
.addGroup(inputJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(spectrumJPanel)
.addGroup(inputJPanelLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addComponent(peptideSequenceJLabel)
.addComponent(peptideSequenceJText, 20, 30 ,30)))
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(peptideSequenceJScrollPane, 20, 40 ,65)
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED)
.addGroup(inputJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(inputJPanelLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addComponent(fragmentIonLbl)
.addComponent(fragmentIonAccuracyTxt, 20, 30 ,30)
.addComponent(precursorIonUnit, 20, 30 ,30))
.addGroup(inputJPanelLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addComponent(startJButton)))
.addGap(15,15,15))
);
allJToolBar.setBackground(new java.awt.Color(255, 255, 255));
allJToolBar.setBorder(null);
allJToolBar.setFloatable(false);
allJToolBar.setRollover(true);
allJToolBar.setBorderPainted(false);
spectrumAnnotationMenuPanel.setLayout(new BoxLayout(spectrumAnnotationMenuPanel, BoxLayout.LINE_AXIS));
allJToolBar.add(spectrumAnnotationMenuPanel);
spectrumShowJPanel.setOpaque(false);
spectrumMainPanel.setOpaque(false);
GroupLayout spectrumMainPanelLayout = new GroupLayout(spectrumShowJPanel);
spectrumShowJPanel.setLayout(spectrumMainPanelLayout);
spectrumMainPanelLayout.setHorizontalGroup(
spectrumMainPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(spectrumMainPanel,GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
spectrumMainPanelLayout.setVerticalGroup(
spectrumMainPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(spectrumMainPanelLayout.createSequentialGroup()
.addComponent(spectrumMainPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
GroupLayout mainJPanelLayout = new GroupLayout(mainJPanel);
mainJPanel.setLayout(mainJPanelLayout);
mainJPanelLayout.setHorizontalGroup(
mainJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(GroupLayout.Alignment.TRAILING, mainJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(mainJPanelLayout.createParallelGroup(GroupLayout.Alignment.TRAILING)
.addComponent(spectrumShowJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(inputJPanel, GroupLayout.Alignment.LEADING, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addContainerGap())
);
mainJPanelLayout.setVerticalGroup(
mainJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(mainJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(inputJPanel, GroupLayout.DEFAULT_SIZE, 140, GroupLayout.DEFAULT_SIZE)
.addPreferredGap(LayoutStyle.ComponentPlacement.RELATED)
.addComponent(spectrumShowJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addContainerGap())
);
GroupLayout layout = new GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGap(0, 1065, Short.MAX_VALUE)
.addGroup(layout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(mainJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
layout.setVerticalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGap(0, 831, Short.MAX_VALUE)
.addGroup(layout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(mainJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
pack();
}
/**
* Modification selections
* @param evt Item event
*/
private void spectrumSourceBoxMouseClicked(ItemEvent evt) {
String selectedSource = String.valueOf(spectrumSourceBox.getSelectedItem());
if (spectrumSourceBox.getSelectedIndex() == 0){
spectrumJPanel.removeAll();
GroupLayout spectrumJPanelLayout = new GroupLayout(spectrumJPanel);
spectrumJPanel.setLayout(spectrumJPanelLayout);
spectrumJPanelLayout.setHorizontalGroup(
spectrumJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(spectrumJPanelLayout.createSequentialGroup()
.addComponent(spectrumFileJLabel, 150, 150, 150)
.addGap(30, 30, 30)
.addComponent(spectrumSourceBox, 90, 90, 90)
.addComponent(spectrumFileJText, GroupLayout.DEFAULT_SIZE, 280, 600)
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(spectrumFileJButton)
.addGap(20, 50, 100))
);
spectrumJPanelLayout.setVerticalGroup(
spectrumJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(spectrumJPanelLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addComponent(spectrumFileJLabel)
.addComponent(spectrumSourceBox, 20, 30 ,30)
.addComponent(spectrumFileJText, 20, 30 ,30)
.addComponent(spectrumFileJButton, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE, GroupLayout.PREFERRED_SIZE))
);
} else {
spectrumJPanel.removeAll();
GroupLayout spectrumJPanelLayout = new GroupLayout(spectrumJPanel);
spectrumJPanel.setLayout(spectrumJPanelLayout);
spectrumJPanelLayout.setHorizontalGroup(
spectrumJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(spectrumJPanelLayout.createSequentialGroup()
.addComponent(spectrumFileJLabel, 150, 150, 150)
.addGap(30, 30, 30)
.addComponent(spectrumSourceBox, 90, 90, 90)
.addComponent(usiIDJText, GroupLayout.DEFAULT_SIZE, 280, 600)
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(getUSIJButton)
.addGap(20, 50, 100))
);
spectrumJPanelLayout.setVerticalGroup(
spectrumJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(spectrumJPanelLayout.createParallelGroup(GroupLayout.Alignment.CENTER)
.addComponent(spectrumFileJLabel)
.addComponent(spectrumSourceBox, 20, 30 ,30)
.addComponent(usiIDJText, 20, 30 ,30)
.addComponent(getUSIJButton, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE, GroupLayout.PREFERRED_SIZE))
);
}
}
private void getUSIJButtonActionPerformed(ActionEvent evt){
String usiID;
if(!usiIDJText.getText().equals("") && usiIDJText.getText() != null){
usiID = usiIDJText.getText();
System.out.println(usiID);
ProgressDialogX progressDialogX = new ProgressDialogX(this,
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMassWait.png")),
true);
progressDialogX.setPrimaryProgressCounterIndeterminate(true);
progressDialogX.setTitle("Searching. Please Wait...");
new Thread(() -> {
try {
progressDialogX.setVisible(true);
} catch (IndexOutOfBoundsException ignored) {
}
}, "searchProgressDialog").start();
new Thread("Searching") {
@Override
public void run() {
try {
String url = "http://proteomecentral.proteomexchange.org/api/proxi/v0.1/spectra?resultType=compact&usi=" + usiID+"&format=json";
URL obj = new URL(url);
int charge = 2;
double precursorMZ = 0.0;
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
// optional default is GET
con.setRequestMethod("GET");
//add request header
con.setRequestProperty("User-Agent", "Mozilla/5.0");
int responseCode = con.getResponseCode();
if (responseCode == 200){
System.out.println("\nSending 'GET' request to URL : " + url);
System.out.println("Response Code : " + responseCode);
BufferedReader in = new BufferedReader(
new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuilder response = new StringBuilder();
while ((inputLine = in.readLine()) != null) {
response.append(inputLine);
}
response.deleteCharAt(0);
response.deleteCharAt(response.length() - 1);
in.close();
JSONObject jsonObject = new JSONObject(response.toString());
JSONArray mzs = jsonObject.getJSONArray("mzs");
JSONArray intensities = jsonObject.getJSONArray("intensities");
JSONArray attributes = jsonObject.getJSONArray("attributes");
for (Object eachAttribute : attributes){
JSONObject jsonAttribute = (JSONObject) eachAttribute;
if (jsonAttribute.getString("accession").equals("MS:1000041")){
charge = Integer.parseInt(jsonAttribute.getString("value"));
} else if (jsonAttribute.getString("accession").equals("MS:1000744")){
precursorMZ = Double.parseDouble((jsonAttribute.getString("value")));
}
}
ArrayList<Charge> charges = new ArrayList<>();
Charge charge1 = new Charge(1, charge);
charges.add(charge1);
Precursor precursor = new Precursor(0, precursorMZ, 0, charges);
generateSpectrum(mzs, intensities, precursor);
} else {
JOptionPane.showMessageDialog(null, "Can not find this spectrum, \n Please check your USI ID.",
"Warning", JOptionPane.WARNING_MESSAGE);
}
progressDialogX.setRunFinished();
//System.out.println(response.toString());
} catch (MalformedURLException e) {
progressDialogX.setRunFinished();
e.printStackTrace();
} catch (ProtocolException e) {
progressDialogX.setRunFinished();
e.printStackTrace();
} catch (IOException e) {
progressDialogX.setRunFinished();
e.printStackTrace();
}
}
}.start();
} else {
JOptionPane.showMessageDialog(null, "Please input valid USI ID.",
"Warning", JOptionPane.WARNING_MESSAGE);
}
}
private void generateSpectrum(JSONArray mzs, JSONArray intensities, Precursor precursor){
HashMap<Double, Peak> peakMap = new HashMap<>();
for(int i = 0; i<mzs.length(); i++){
Peak peak = new Peak(mzs.getDouble(i), intensities.getDouble(i));
peakMap.put(mzs.getDouble(i), peak);
}
currentSpectrum = new MSnSpectrum(2, precursor, "1", peakMap, "test");
validateInput();
}
/**
* Open a new database results display frame
* @param evt Mouse click event
*/
private void newJMenuItemActionPerformed(ActionEvent evt){
int value = JOptionPane.showConfirmDialog(this,
"Do you want to display database results ?",
"Give up current",
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
if (value == JOptionPane.YES_OPTION) {
PDVMainClass pdvMainClass = new PDVMainClass(true);
new DatabaseImportDialog(pdvMainClass, true, this);
} else if (value == JOptionPane.NO_OPTION || value == JOptionPane.CLOSED_OPTION) {
}
}
/**
* Open new De Novo results display
* @param evt Mouse click event
*/
private void openDenovoJMenuItemActionPerformed(ActionEvent evt){
int value = JOptionPane.showConfirmDialog(this,
"Do you want to display De novo results ?",
"Give up current",
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
if (value == JOptionPane.YES_OPTION) {
new DeNovoImportDialog(this, true, this);
} else if (value == JOptionPane.NO_OPTION || value == JOptionPane.CLOSED_OPTION) {
}
}
/**
* Exist
* @param evt Mouse click event
*/
private void exitJMenuItemActionPerformed(ActionEvent evt){
formWindowClosing(null);
}
/**
* Select a mgf file with only one single spectral
* @param evt mouse click event
*/
private void spectrumFileJButtonActionPerformed(ActionEvent evt) {
JFileChooser fileChooser = new JFileChooser(lastSelectedFolder.getLastSelectedFolder());
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.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.setLastSelectedFolder(selectedFile.getParent());
}
}
spectrumFileJText.setText(spectrumFile.getName() + " file selected.");
validateInput();
}
}
/**
* PeptideSequenceJTextKeyReleased
* @param evt Key event
*/
private void peptideSequenceJTextKeyReleased(KeyEvent evt){
peptideSequence = peptideSequenceJText.getText();
if (peptideSequence.matches("[A-Za-z]+")){
Font font = new Font("Arial bold",Font.PLAIN,16);
if(peptideSequence != null && peptideSequence.length() != 0 && !peptideSequence.contains(" ")){
peptideSequence = peptideSequenceJText.getText().toUpperCase();
peptideSequenceJText.setText(peptideSequence);
allButtons = new ArrayList<>();
peptideSequenceJPanel.removeAll();
peptideSequenceJPanel.setOpaque(true);
peptideSequenceJPanel.setBackground(Color.WHITE);
peptideSequenceJScrollPane.setBackground(Color.WHITE);
peptideSequenceJScrollPane.setVisible(true);
String[] peptideArray = peptideSequence.split("");
ArrayList<String> peptideList = new ArrayList<>();
peptideList.add("NH-");
for(String eachOriAA: peptideArray){
peptideList.add(eachOriAA);
}
peptideList.add("-COOH");
for(String eachAA: peptideList){
JButton eachAAJButton = new JButton(eachAA);
eachAAJButton.setBorder(null);
eachAAJButton.setBorderPainted(false);
eachAAJButton.setContentAreaFilled(false);
eachAAJButton.setOpaque(false);
eachAAJButton.setPreferredSize(new Dimension(40,40));
if(peptideList.indexOf(eachAA) == peptideList.size()-1){
eachAAJButton.setPreferredSize(new Dimension(60,40));
}
eachAAJButton.setFont(font);
allButtons.add(eachAAJButton);
peptideSequenceJPanel.add(eachAAJButton);
eachAAJButton.addActionListener(this::eachAAJButtonActionPerformed);
}
peptideSequenceJScrollPane.setOpaque(true);
peptideSequenceJScrollPane.setViewportView(peptideSequenceJPanel);
inputJPanel.revalidate();
inputJPanel.repaint();
}
} else {
JOptionPane.showMessageDialog(this, JOptionEditorPane.getJOptionEditorPane(
"Please input correct peptide sequence."),
"Format Error", JOptionPane.WARNING_MESSAGE);
}
indexOfModification.clear();
modificationMatches.clear();
validateInput();
}
/**
* EachAAJButtonActionPerformed
* @param evt Mouse click event
*/
private void eachAAJButtonActionPerformed(ActionEvent evt) {
JButton jButton = (JButton) evt.getSource();
showSingleAAModification(jButton);
}
/**
* Set modification for selected amino acid
* @param singleModification Modification
* @param aAJButton JButton
*/
public void setSingleModification(String singleModification, JButton aAJButton, Boolean userInput){
Integer aASite = allButtons.indexOf(aAJButton);
String aAName = aAJButton.getText();
if(!singleModification.equals("null")){
ModificationMatch modificationMatch;
if (userInput){
String modificationName;
PTM ptm;
ArrayList<String> residues = new ArrayList<>();
residues.add(aAName);
if(aAName.equals("NH-")){
modificationName = singleModification + " of N-term";
if (!ptmFactory.containsPTM(modificationName)){
ptm = new PTM(PTM.MODNP, modificationName, Double.valueOf(singleModification), null);
ptm.setShortName(singleModification);
ptmFactory.addUserPTM(ptm);
}
} else if(aAName.equals("-COOH")){
modificationName = singleModification + " of C-term";
if (!ptmFactory.containsPTM(modificationName)){
ptm = new PTM(PTM.MODCP, modificationName, Double.valueOf(singleModification), null);
ptm.setShortName(singleModification);
ptmFactory.addUserPTM(ptm);
}
} else {
modificationName = singleModification + " of " + aAName;
if (!ptmFactory.containsPTM(modificationName)){
ptm = new PTM(PTM.MODAA, modificationName, Double.valueOf(singleModification), residues);
ptm.setShortName(singleModification);
ptmFactory.addUserPTM(ptm);
}
}
singleModification = modificationName;
}
if(aAName.equals("NH-")){
modificationMatch = new ModificationMatch(singleModification, false, 1);
}else if(aAName.equals("-COOH")){
modificationMatch = new ModificationMatch(singleModification, false, aASite - 1);
}else {
modificationMatch = new ModificationMatch(singleModification, false, aASite);
}
aAJButton.setBackground(Color.blue);
aAJButton.setForeground(Color.blue);
aAJButton.setToolTipText(modificationMatch.getTheoreticPtm());
if(indexOfModification.contains(aASite)){
modificationMatches.remove(indexOfModification.indexOf(aASite));
indexOfModification.remove(aASite);
indexOfModification.add(aASite);
modificationMatches.add(modificationMatch);
}else {
indexOfModification.add(aASite);
modificationMatches.add(modificationMatch);
}
}else {
aAJButton.setBackground(Color.BLACK);
aAJButton.setForeground(Color.BLACK);
aAJButton.setToolTipText("Click the amino acid to select modification");
if(indexOfModification.contains(aASite)){
modificationMatches.remove(indexOfModification.indexOf(aASite));
indexOfModification.remove(aASite);
}
}
}
/**
* Show all modifications of one single amino acid for selected button
* @param aAJButton JButton
*/
private void showSingleAAModification(JButton aAJButton){
String aAName = aAJButton.getText();
ArrayList<String> singleModifications = new ArrayList<>();
if (aAName == "NH-"){
singleModifications.addAll(aASingleModification.get("N-terminus"));
}else if(aAName == "-COOH"){
singleModifications.addAll(aASingleModification.get("C-terminus"));
}else {
singleModifications = aASingleModification.get(aAName);
}
if(singleModifications != null){
Collections.sort(singleModifications);
String[] singleModificationsArray = singleModifications.toArray(new String[0]);
new ModificationDialog(this, aAJButton, singleModificationsArray);
}
}
/**
* Get all modifications as map
* @return HashMap
*/
public HashMap<String, ArrayList< String >> getModification(){
HashMap<String, ArrayList< String > > modificationMass = new HashMap<>();
for (int i = 0;i<300;i++){
ArrayList<String> orderedModifications = ptmFactory.getPTMs();
if (orderedModifications.size() >300){
for (String modificationName : orderedModifications){
String[] modificationNameSplit = String.valueOf(ptmFactory.getPTM(modificationName)).split(" ");
String aminoAcidName = modificationNameSplit[modificationNameSplit.length-1];
if(modificationMass.containsKey(aminoAcidName)){
modificationMass.get(aminoAcidName).add(modificationName);
}else {
ArrayList< String > singleModi = new ArrayList<>();
singleModi.add(modificationName);
modificationMass.put(aminoAcidName, singleModi);
}
}
break;
}else{
ptmFactory = PTMFactory.getInstance();
try {Thread.sleep(1000);
} catch (InterruptedException e) {
e.printStackTrace();
}
}
}
return modificationMass;
}
/**
* Start annotating according to spectrum and peptide details
* @param evt Mouse click event
*/
private void startJButtonActionPerformed(ActionEvent evt) {
SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
ArrayList<String > spectrumTitle;
Double fragmentIonMZTolerance = 0.05;
if (fragmentIonAccuracyTxt.getText()!= ""){
fragmentIonMZTolerance = Double.valueOf(fragmentIonAccuracyTxt.getText());
}else {
fragmentIonMZTolerance = 0.05;
}
SpectrumPanel.setIonColor(Ion.getGenericIon(Ion.IonType.PEPTIDE_FRAGMENT_ION, 1), new Color(0, 153, 0));
SpectrumPanel.setIonColor(Ion.getGenericIon(Ion.IonType.PEPTIDE_FRAGMENT_ION, 4), new Color(255, 102, 0));
SearchParameters.MassAccuracyType fragmentAccuracyType = SearchParameters.MassAccuracyType.DA;
if(precursorIonUnit.getSelectedIndex() == 0){
fragmentAccuracyType = SearchParameters.MassAccuracyType.DA;
}else {
fragmentAccuracyType = SearchParameters.MassAccuracyType.PPM;
}
if (searchParameters == null) {
searchParameters = new SearchParameters();
searchParameters.setDigestionPreferences(DigestionPreferences.getDefaultPreferences());
}
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.setPtmSettings(ptmSettings);
searchParameters.setFragmentAccuracyType(fragmentAccuracyType);
searchParameters.setFragmentIonAccuracy(fragmentIonMZTolerance);
annotationSettings.setPreferencesFromSearchParameters(searchParameters);
spectrumMainPanel.updateSearchParameters(searchParameters);
spectrumMainPanel.setShowDetails(false);
spectrumMainPanel.setAnnotationSettings(annotationSettings);
Peptide peptide = new Peptide(peptideSequence, modificationMatches);
peptideAssumption = new PeptideAssumption(peptide, 1, 1, new Charge(1,1), 0, null);
try {
if (spectrumSourceBox.getSelectedIndex() == 0){
spectrumFactory.addSpectra(spectrumFile);
spectrumTitle = spectrumFactory.getSpectrumTitles(spectrumFile.getName());
currentSpectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumFile.getName(), spectrumTitle.get(0));
}
int charge = currentSpectrum.getPrecursor().getPossibleCharges().get(0).value;
peptideAssumption.setIdentificationCharge(new Charge(1, charge));
switchPaneMenu.setEnabled(true);
updateSpectrum();
} catch (IOException e) {
e.printStackTrace();
} catch (ClassNotFoundException e) {
e.printStackTrace();
} catch (MzMLUnmarshallerException e) {
e.printStackTrace();
}
}
/**
* Update spectrum
*/
private void updateSpectrum(){
TitledBorder titledBorder = BorderFactory.createTitledBorder(peptideAssumption.getPeptide().getTaggedModifiedSequence(searchParameters.getPtmSettings(), false, false, false, false) + " \t ");
titledBorder.setTitleFont(new Font("Console", Font.PLAIN, 12));
spectrumShowJPanel.setBorder(titledBorder);
SpectrumMatch spectrumMatch = new SpectrumMatch();
spectrumMatch.setBestPeptideAssumption(peptideAssumption);
spectrumMainPanel.updateSpectrum(spectrumMatch.getBestPeptideAssumption(), currentSpectrum, "1");
spectrumShowJPanel.revalidate();
spectrumShowJPanel.repaint();
}
/**
* Validates the input and enable start button
*/
private void validateInput() {
boolean allValid = true;
if (spectrumFile != null) {
spectrumFileJLabel.setForeground(Color.BLACK);
spectrumFileJLabel.setToolTipText(null);
} else {
spectrumFileJLabel.setForeground(Color.RED);
spectrumFileJLabel.setToolTipText("Please select the spectrum file");
spectrumFileJText.setToolTipText("Please select the spectrum file");
spectrumFileJText.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
allValid = false;
}
if (currentSpectrum != null){
allValid = true;
}
if(peptideSequence != null && peptideSequence.length() != 0 && !peptideSequence.contains(" ")){
peptideSequenceJLabel.setForeground(Color.BLACK);
peptideSequenceJLabel.setToolTipText(null);
}else {
peptideSequenceJLabel.setForeground(Color.RED);
peptideSequenceJLabel.setToolTipText("Please input one peptide");
peptideSequenceJText.setToolTipText("Please input one peptide");
allValid = false;
}
startJButton.setEnabled(allValid);
}
/**
* Close frame
* @param evt Window event
*/
private void formWindowClosing(WindowEvent evt) {
close();
}
/**
* Close
*/
public void close() {
if (this.getExtendedState() == Frame.ICONIFIED || !this.isActive()) {
this.setExtendedState(Frame.MAXIMIZED_BOTH);
}
int value = JOptionPane.showConfirmDialog(this,
"Do you want to give up it and close PDV? ",
"Close PDV",
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
if (value == JOptionPane.YES_OPTION) {
closePDV();
} else if (value == JOptionPane.NO_OPTION) {
}
}
/**
* Close PDV
*/
private void closePDV(){
exceptionHandler.setIgnoreExceptions(true);
progressDialog = new ProgressDialogX(this,
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMassWait.png")),
true);
progressDialog.getProgressBar().setStringPainted(false);
progressDialog.getProgressBar().setIndeterminate(true);
progressDialog.setTitle("Closing. Please Wait...");
final SinglePeptideDisplay singlePeptideDisplay = this;
new Thread(() -> {
try {
progressDialog.setVisible(true);
} catch (IndexOutOfBoundsException e) {
// ignore
}
}, "ProgressDialog").start();
SwingUtilities.invokeLater(() -> {
try {
if (!progressDialog.isRunCanceled()) {
TempFilesManager.deleteTempFolders();
}
} catch (Exception e) {
e.printStackTrace();
catchException(e);
} finally {
progressDialog.setRunFinished();
singlePeptideDisplay.setVisible(false);
System.exit(0);
}
});
}
/**
* Catch exception
* @param e Exception
*/
private void catchException(Exception e) {
exceptionHandler.catchException(e);
}
}
