package PDVGUI.gui;
import PDVGUI.gui.utils.FileImport.PrideXMLImportDialog;
import PDVGUI.gui.utils.InfoPanel;
import PDVGUI.gui.utils.SpectrumMainPanel;
import com.compomics.util.experiment.biology.PTM;
import com.compomics.util.experiment.biology.PTMFactory;
import com.compomics.util.experiment.biology.Peptide;
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_assumptions.PeptideAssumption;
import com.compomics.util.experiment.massspectrometry.*;
import com.compomics.util.experiment.massspectrometry.Precursor;
import uk.ac.ebi.pride.jaxb.model.*;
import uk.ac.ebi.pride.jaxb.model.Spectrum;
import uk.ac.ebi.pride.jaxb.xml.PrideXmlReader;
import javax.swing.*;
import javax.swing.border.TitledBorder;
import javax.swing.event.ChangeEvent;
import javax.swing.event.TreeSelectionEvent;
import javax.swing.table.DefaultTableModel;
import javax.swing.table.JTableHeader;
import javax.swing.table.TableCellRenderer;
import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.DefaultTreeModel;
import javax.swing.tree.TreeNode;
import javax.swing.tree.TreeSelectionModel;
import java.awt.*;
import java.awt.event.*;
import java.util.*;
import java.util.List;
/**
* PrideXML result display
* Created by Ken on 9/14/2017.
*/
public class PrideXMLDisplay extends JFrame {
private JPanel psmJPanel;
private JPanel spectrumShowJPanel;
private JPanel spectrumTableJPanel;
private JPanel treeJPanel;
private JSplitPane allJSplitPane;
private JSplitPane tabelAndChartJSplit;
private JSplitPane treeAndDetailJSplit;
private JTable psmJTable;
private JTable spectrumJTable;
private JButton openSidebarJButton;
private JTabbedPane pSMSpectrumJTabbedpane;
private JComboBox precursorIonUnit;
private JTextField fragmentIonAccuracyTxt;
/**
* PSMTable tooltips list
*/
private ArrayList<String> psmJTableToolTips;
/**
* Spectrum table tooltips list
*/
private ArrayList<String> spectrumJTableToolTips;
/**
* PrideXMLReader List
*/
public HashMap<String, PrideXmlReader> titleToPrideXmlReader = new HashMap<>();
/**
* Accession to ID
*/
private HashMap<String, String> accessionToId = new HashMap<>();
/**
* Current prideXML reader
*/
private PrideXmlReader currentPrideXmlReader;
/**
* Current protein
*/
private String currentProtein;
/**
* PTM factory
*/
private PTMFactory ptmFactory = PTMFactory.getInstance();
/**
* Current peptide list
*/
private ArrayList<Peptide> currentPeptideList = new ArrayList<>();
/**
* Current peptide item list
*/
private List<PeptideItem> currentPeptideItemList;
/**
* Search parameters
*/
public SearchParameters searchParameters = new SearchParameters();
/**
* Spectrum main panel
*/
private SpectrumMainPanel spectrumMainPanel;
/**
* New spectrum main panel
*/
private SpectrumMainPanel onlySpectrumMainPanel;
/**
* Current table match list
*/
private ArrayList< SpectrumMatch> currentTableMatchList = new ArrayList<>();
/**
* Current MZ list
*/
private ArrayList<Double> currentMz = new ArrayList<>();
/**
* Current file count
*/
private Integer currentFileCount = 0;
/**
* Current protein count
*/
private Integer currentProteinCount = 0;
/**
* Selected psm key
*/
private String selectedPSMKey;
/**
* Current spectrum
*/
private MSnSpectrum currentSpectrum;
/**
* Current table psm key list
*/
private ArrayList<String> currentTablePSMKeyList = new ArrayList<>();
/**
* Information panel
*/
private InfoPanel infoPanel = new InfoPanel();
/**
* Constructor
* @param pdvStart Parent class
*/
public PrideXMLDisplay(PDVStart pdvStart) {
setUpTableHeaderToolTips();
spectrumMainPanel = new SpectrumMainPanel(this);
onlySpectrumMainPanel = new SpectrumMainPanel(this);
initComponent();
setExtendedState(JFrame.MAXIMIZED_BOTH);
if (pdvStart != null) {
pdvStart.setVisible(false);
}
setIconImage(Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")));
setVisible(true);
new PrideXMLImportDialog(this);
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);
}
/**
* Set spectrum table tooltips
*/
private void setUpTableHeaderToolTips() {
psmJTableToolTips = new ArrayList<>();
psmJTableToolTips.add("Spectrum key");
psmJTableToolTips.add("Peptide Sequence");
psmJTableToolTips.add("Spectrum key in Spectrum File");
psmJTableToolTips.add("Precursor Charge");
psmJTableToolTips.add("Precursor m/z");
psmJTableToolTips.add("Retention Time");
psmJTableToolTips.add("Comments");
spectrumJTableToolTips = new ArrayList<>();
spectrumJTableToolTips.add("Spectrum key in spectrum file");
spectrumJTableToolTips.add("MS level");
spectrumJTableToolTips.add("Precursor charge");
spectrumJTableToolTips.add("Precursor m/z");
spectrumJTableToolTips.add("RT range start");
spectrumJTableToolTips.add("RT rang stop");
spectrumJTableToolTips.add("Peaks number");
spectrumJTableToolTips.add("Intensity sum");
spectrumJTableToolTips.add("Identified or not");
}
/**
* Init all GUI components
*/
private void initComponent() {
JPanel mainJPanel = new JPanel();
JPanel backJPanel = new JPanel();
JPanel sideJPanel = new JPanel();
JPanel settingJPanel = new JPanel();
JButton setButton = new JButton();
JLabel splitJLabel1 = new JLabel(" | ");
JLabel splitJLabel2 = new JLabel(" | ");
JMenuBar menuBar = new JMenuBar();
JMenu fileJMenu = new JMenu();
JMenuItem exitJMenuItem = new JMenuItem();
JLabel fragmentIonAccuracyJLabel = new JLabel("Fragment m/z Tolerance: ");
JLabel fragmentIonType1Lbl = new JLabel("Unit: ");
JScrollPane inforJScrollPane = new JScrollPane();
JScrollPane psmsScrollPane = new JScrollPane();
JScrollPane spectrumTableScrollPane = new JScrollPane();
JPanel detailsJPanel = new JPanel();
JButton addNewJButton = new JButton();
allJSplitPane = new JSplitPane();
tabelAndChartJSplit = new JSplitPane();
spectrumShowJPanel = new JPanel();
pSMSpectrumJTabbedpane = new JTabbedPane();
fragmentIonAccuracyTxt = new JTextField("0.05");
precursorIonUnit = new JComboBox();
psmJPanel = new JPanel();
spectrumTableJPanel = new JPanel();
treeAndDetailJSplit = new JSplitPane();
treeJPanel = new JPanel();
openSidebarJButton = new JButton();
psmJTable = new JTable() {
protected JTableHeader createDefaultTableHeader() {
return new JTableHeader(columnModel) {
public String getToolTipText(MouseEvent e) {
Point p = e.getPoint();
int index = columnModel.getColumnIndexAtX(p.x);
int realIndex = columnModel.getColumn(index).getModelIndex();
return psmJTableToolTips.get(realIndex);
}
};
}
public Component prepareRenderer(TableCellRenderer renderer, int row, int column) {
Component component = super.prepareRenderer(renderer, row, column);
if (row % 2 == 0) {
component.setBackground(Color.white);
} else {
component.setBackground(new Color(164, 233, 255));
}
if (isRowSelected(row)) {
component.setBackground(new Color(20, 20, 40));
}
if (String.valueOf(getValueAt(row, column)).contains(" Rank:" + " <html>" + 1)) {
component.setBackground(new Color(255, 116, 135));
}
return component;
}
};
psmJTable.setRowHeight(20);
psmJTable.setFont(new Font("Arial", Font.PLAIN, 12));
psmJTable.getTableHeader().setFont(new Font("Dialog", 0, 13));
psmJTable.setAutoCreateRowSorter(true);
spectrumJTable = new JTable() {
protected JTableHeader createDefaultTableHeader() {
return new JTableHeader(columnModel) {
public String getToolTipText(MouseEvent e) {
Point p = e.getPoint();
int index = columnModel.getColumnIndexAtX(p.x);
int realIndex = columnModel.getColumn(index).getModelIndex();
return spectrumJTableToolTips.get(realIndex);
}
};
}
public Component prepareRenderer(TableCellRenderer renderer, int row, int column) {
Component component = super.prepareRenderer(renderer, row, column);
if (row % 2 == 0) {
component.setBackground(Color.white);
} else {
component.setBackground(new Color(164, 233, 255));
}
if (isRowSelected(row)) {
component.setBackground(new Color(20, 20, 40));
}
if (String.valueOf(getValueAt(row, column)).contains(" Rank:" + " <html>" + 1)) {
component.setBackground(new Color(255, 116, 135));
}
return component;
}
};
spectrumJTable.setRowHeight(20);
spectrumJTable.setFont(new Font("Arial", Font.PLAIN, 12));
spectrumJTable.getTableHeader().setFont(new Font("Dialog", 0, 13));
spectrumJTable.setAutoCreateRowSorter(true);
setDefaultCloseOperation(javax.swing.WindowConstants.DO_NOTHING_ON_CLOSE);
setTitle("PDV - PrideXML Display");
setBackground(new java.awt.Color(255, 255, 255));
setMinimumSize(new java.awt.Dimension(760, 600));
addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent evt) {
formWindowClosing(evt);
}
});
mainJPanel.setBackground(new java.awt.Color(255, 255, 255));
mainJPanel.setOpaque(true);
mainJPanel.setPreferredSize(new java.awt.Dimension(1260, 800));
exitJMenuItem.setMnemonic('E');
exitJMenuItem.setText("Exit");
exitJMenuItem.addActionListener(this::exitJMenuItemActionPerformed);
fileJMenu.add(exitJMenuItem);
fileJMenu.setMnemonic('F');
fileJMenu.setText("File");
menuBar.add(fileJMenu);
sideJPanel.setBackground(new Color(217, 248, 255));
sideJPanel.setMinimumSize(new Dimension(20, 0));
sideJPanel.setOpaque(false);
sideJPanel.setLayout(new BoxLayout(sideJPanel, BoxLayout.Y_AXIS));
openSidebarJButton.setIcon(new ImageIcon(getClass().getResource("/icons/fold.png")));
openSidebarJButton.setToolTipText("Fold the side tree.");
openSidebarJButton.setBorder(null);
openSidebarJButton.setBorderPainted(false);
openSidebarJButton.setContentAreaFilled(false);
openSidebarJButton.setSelected(true);
openSidebarJButton.addActionListener(this::openSidebarJButtonActionPerform);
addNewJButton.setIcon(new ImageIcon(getClass().getResource("/icons/add.png")));
addNewJButton.setBorder(null);
addNewJButton.setBorderPainted(false);
addNewJButton.setContentAreaFilled(false);
addNewJButton.setToolTipText("Add more pride XML files.");
addNewJButton.addActionListener(this::addNewJButtonActionPerform);
sideJPanel.add(openSidebarJButton);
sideJPanel.add(addNewJButton);
precursorIonUnit.setModel(new DefaultComboBoxModel(new String[]{"Da", "ppm"}));
precursorIonUnit.setMaximumSize(new Dimension(50, 20));
precursorIonUnit.setBackground(Color.WHITE);
fragmentIonAccuracyTxt.setHorizontalAlignment(SwingConstants.CENTER);
fragmentIonAccuracyTxt.setMaximumSize(new Dimension(40, 20));
setButton.setIcon(new ImageIcon(getClass().getResource("/icons/update.png")));
setButton.setBorder(null);
setButton.setBorderPainted(false);
setButton.setContentAreaFilled(false);
setButton.setToolTipText("Set New setting");
setButton.addActionListener(this::setButtonActionPerform);
settingJPanel.setBackground(new Color(255, 255, 255));
settingJPanel.setMinimumSize(new Dimension(20, 0));
settingJPanel.setOpaque(false);
settingJPanel.setLayout(new BoxLayout(settingJPanel, BoxLayout.X_AXIS));
fragmentIonAccuracyJLabel.setFont(new Font("Arial", Font.PLAIN, 12));
fragmentIonType1Lbl.setFont(new Font("Arial", Font.PLAIN, 12));
settingJPanel.add(splitJLabel2);
settingJPanel.add(fragmentIonAccuracyJLabel);
settingJPanel.add(fragmentIonAccuracyTxt);
settingJPanel.add(splitJLabel1);
settingJPanel.add(fragmentIonType1Lbl);
settingJPanel.add(precursorIonUnit);
settingJPanel.add(setButton);
allJSplitPane.setBorder(null);
allJSplitPane.setDividerLocation(0.2);
allJSplitPane.setDividerSize(5);
allJSplitPane.setOrientation(JSplitPane.HORIZONTAL_SPLIT);
allJSplitPane.setResizeWeight(0.5);
allJSplitPane.setOpaque(false);
allJSplitPane.setContinuousLayout(true);
treeAndDetailJSplit.setBorder(null);
treeAndDetailJSplit.setDividerLocation(0.4);
treeAndDetailJSplit.setDividerSize(5);
treeAndDetailJSplit.setOrientation(JSplitPane.VERTICAL_SPLIT);
treeAndDetailJSplit.setResizeWeight(0.5);
treeAndDetailJSplit.setOpaque(false);
treeAndDetailJSplit.setVisible(true);
treeAndDetailJSplit.setContinuousLayout(true);
TitledBorder titledBorder = BorderFactory.createTitledBorder("Pride XML file(s)" + " \t ");
titledBorder.setTitleFont(new Font("Console", Font.PLAIN, 12));
treeJPanel.setBorder(titledBorder);
treeJPanel.setOpaque(false);
treeAndDetailJSplit.setTopComponent(treeJPanel);
detailsJPanel.setOpaque(false);
detailsJPanel.setBorder(BorderFactory.createTitledBorder("Details"));
GroupLayout detailsJPanelLayout = new GroupLayout(detailsJPanel);
detailsJPanel.setLayout(detailsJPanelLayout);
detailsJPanelLayout.setHorizontalGroup(
detailsJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(detailsJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(infoPanel, GroupLayout.DEFAULT_SIZE, 300, Short.MAX_VALUE)
.addContainerGap())
);
detailsJPanelLayout.setVerticalGroup(
detailsJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(detailsJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(infoPanel, GroupLayout.DEFAULT_SIZE, 490, Short.MAX_VALUE)
.addContainerGap())
);
treeAndDetailJSplit.setRightComponent(detailsJPanel);
allJSplitPane.setTopComponent(treeAndDetailJSplit);
titledBorder = BorderFactory.createTitledBorder("PSM Table" + " \t ");
titledBorder.setTitleFont(new Font("Console", Font.PLAIN, 12));
psmJPanel.setBorder(titledBorder);
psmJPanel.setOpaque(false);
psmJTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
psmJTable.addMouseListener(new MouseAdapter() {
public void mouseExited(MouseEvent evt) {
psmJTableMouseExited(evt);
}
public void mouseReleased(MouseEvent evt) {
psmJTableMouseReleased(evt);
}
});
psmJTable.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(KeyEvent evt) {
psmJTableKeyReleased(evt);
}
});
psmsScrollPane.setBackground(Color.white);
psmsScrollPane.setOpaque(true);
psmsScrollPane.setViewportView(psmJTable);
psmJTable.getAccessibleContext().setAccessibleName("psmJTable");
GroupLayout psmJPanelLayout = new GroupLayout(psmJPanel);
psmJPanel.setLayout(psmJPanelLayout);
psmJPanelLayout.setHorizontalGroup(
psmJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(psmsScrollPane, GroupLayout.DEFAULT_SIZE, 800, Short.MAX_VALUE)
);
psmJPanelLayout.setVerticalGroup(
psmJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(psmsScrollPane, GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE)
);
pSMSpectrumJTabbedpane.addChangeListener(this::pSMSpectrumJTabbedpaneStateChanged);
pSMSpectrumJTabbedpane.setOpaque(false);
pSMSpectrumJTabbedpane.add(psmJPanel, "PSM");
titledBorder = BorderFactory.createTitledBorder("Spectrum Table" + " \t ");
titledBorder.setTitleFont(new Font("Console", Font.PLAIN, 12));
spectrumTableJPanel.setBorder(titledBorder);
spectrumTableJPanel.setOpaque(false);
spectrumJTable.setOpaque(false);
spectrumJTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
spectrumJTable.addMouseListener(new MouseAdapter() {
public void mouseExited(MouseEvent evt) {
spectrumJTableMouseExited(evt);
}
public void mouseReleased(MouseEvent evt) {
spectrumJTableMouseReleased(evt);
}
});
spectrumJTable.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(KeyEvent evt) {
spectrumJTableKeyReleased(evt);
}
});
spectrumTableScrollPane.setViewportView(spectrumJTable);
spectrumTableScrollPane.setOpaque(false);
spectrumJTable.getAccessibleContext().setAccessibleName("spectrumJTable");
GroupLayout spectrumTableJPanelLayout = new GroupLayout(spectrumTableJPanel);
spectrumTableJPanel.setLayout(spectrumTableJPanelLayout);
spectrumTableJPanelLayout.setHorizontalGroup(
spectrumTableJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(spectrumTableScrollPane, GroupLayout.DEFAULT_SIZE, 600, Short.MAX_VALUE)
);
spectrumTableJPanelLayout.setVerticalGroup(
spectrumTableJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(spectrumTableScrollPane, GroupLayout.DEFAULT_SIZE, 400, Short.MAX_VALUE)
);
pSMSpectrumJTabbedpane.add(spectrumTableScrollPane, "Spectrum");
tabelAndChartJSplit.setBorder(null);
tabelAndChartJSplit.setDividerLocation(0.4);
tabelAndChartJSplit.setDividerSize(5);
tabelAndChartJSplit.setOrientation(JSplitPane.VERTICAL_SPLIT);
tabelAndChartJSplit.setResizeWeight(0.5);
tabelAndChartJSplit.setOpaque(false);
tabelAndChartJSplit.setContinuousLayout(true);
tabelAndChartJSplit.setTopComponent(pSMSpectrumJTabbedpane);
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))
);
tabelAndChartJSplit.setRightComponent(spectrumShowJPanel);
allJSplitPane.setRightComponent(tabelAndChartJSplit);
backJPanel.setBackground(Color.WHITE);
backJPanel.setOpaque(false);
GroupLayout backJPanelLayout = new GroupLayout(backJPanel);
backJPanel.setLayout(backJPanelLayout);
backJPanelLayout.setHorizontalGroup(
backJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(backJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(sideJPanel, GroupLayout.DEFAULT_SIZE, 20, 20)
.addComponent(allJSplitPane, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addContainerGap())
);
backJPanelLayout.setVerticalGroup(
backJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(backJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(backJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(sideJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(allJSplitPane, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addContainerGap())
);
GroupLayout mainJPanelLayout = new GroupLayout(mainJPanel);
mainJPanel.setLayout(mainJPanelLayout);
mainJPanelLayout.setHorizontalGroup(
mainJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(settingJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(backJPanel)
);
mainJPanelLayout.setVerticalGroup(
mainJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(mainJPanelLayout.createSequentialGroup()
.addComponent(settingJPanel, 25, 25, 25)
.addComponent(backJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
setJMenuBar(menuBar);
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(mainJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(mainJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
String motif;
String os = System.getProperty("os.name");
if(os.toLowerCase().startsWith("win")){
motif="com.sun.java.swing.plaf.windows.WindowsLookAndFeel";
} else if (os.toLowerCase().startsWith("mac")){
motif="com.sun.java.swing.plaf.mac.MacLookAndFeel";
} else {
motif=UIManager.getSystemLookAndFeelClassName();
}
try {
UIManager.setLookAndFeel(motif);
} catch (ClassNotFoundException | InstantiationException | UnsupportedLookAndFeelException | IllegalAccessException e) {
e.printStackTrace();
}
SwingUtilities.updateComponentTreeUI(this);
pack();
}
/**
* Close the program when click exist
*
* @param evt Window event
*/
private void formWindowClosing(WindowEvent evt) {
close();
}
/**
* Close dialog
*/
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 " + " 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 the program
*/
private void closePDV() {
System.exit(0);
}
/**
* exitJMenuItemActionPerformed
* @param evt Mouse click event
*/
private void exitJMenuItemActionPerformed(ActionEvent evt){
close();
}
/**
* openSidebarJButtonActionPerform
* @param evt Mouse click event
*/
private void openSidebarJButtonActionPerform(ActionEvent evt){
if(treeAndDetailJSplit.isVisible()){
openSidebarJButton.setIcon(new ImageIcon(getClass().getResource("/icons/unfold.png")));
treeAndDetailJSplit.setVisible(false);
allJSplitPane.setDividerSize(0);
allJSplitPane.revalidate();
allJSplitPane.repaint();
} else {
openSidebarJButton.setIcon(new ImageIcon(getClass().getResource("/icons/fold.png")));
treeAndDetailJSplit.setVisible(true);
allJSplitPane.setDividerSize(5);
allJSplitPane.setDividerLocation(0.2);
allJSplitPane.revalidate();
allJSplitPane.repaint();
}
}
/**
* addNewJButtonActionPerform
* @param evt Mouse click event
*/
private void addNewJButtonActionPerform(ActionEvent evt){
new PrideXMLImportDialog(this);
}
/**
* setButtonActionPerform
* @param evt Mouse click event
*/
private void setButtonActionPerform(ActionEvent evt){
Double fragmentIonMZTolerance = 0.05;
if(fragmentIonAccuracyTxt.getText() != "" && fragmentIonAccuracyTxt.getText() != null){
fragmentIonMZTolerance = Double.valueOf(fragmentIonAccuracyTxt.getText());
}
if(precursorIonUnit.getSelectedIndex() == 0){
searchParameters.setFragmentAccuracyType(SearchParameters.MassAccuracyType.DA);
}else {
searchParameters.setFragmentAccuracyType(SearchParameters.MassAccuracyType.PPM);
}
searchParameters.setFragmentIonAccuracy(fragmentIonMZTolerance);
spectrumMainPanel.setFragmentIonAccuracy(searchParameters.getFragmentAccuracyType(), fragmentIonMZTolerance);
}
/**
* pSMSpectrumJTabbedpaneStateChanged
* @param evt Mouse click event
*/
private void pSMSpectrumJTabbedpaneStateChanged(ChangeEvent evt) {
int index = pSMSpectrumJTabbedpane.getSelectedIndex();
spectrumShowJPanel.removeAll();
switch (index) {
case 0:
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))
);
tabelAndChartJSplit.addPropertyChangeListener(JSplitPane.DIVIDER_LOCATION_PROPERTY,
evt1 -> spectrumMainPanel.updateSpectrum());
allJSplitPane.addPropertyChangeListener(JSplitPane.DIVIDER_LOCATION_PROPERTY,
evt12 -> spectrumMainPanel.updateSpectrum());
break;
case 1:
GroupLayout spectrumMainPanelLayout1 = new GroupLayout(spectrumShowJPanel);
spectrumShowJPanel.setLayout(spectrumMainPanelLayout1);
spectrumMainPanelLayout1.setHorizontalGroup(
spectrumMainPanelLayout1.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(onlySpectrumMainPanel,GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
spectrumMainPanelLayout1.setVerticalGroup(
spectrumMainPanelLayout1.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(spectrumMainPanelLayout1.createSequentialGroup()
.addComponent(onlySpectrumMainPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
spectrumJTableMouseReleased(null);
tabelAndChartJSplit.addPropertyChangeListener(JSplitPane.DIVIDER_LOCATION_PROPERTY,
evt13 -> onlySpectrumMainPanel.updateSpectrum(currentSpectrum));
allJSplitPane.addPropertyChangeListener(JSplitPane.DIVIDER_LOCATION_PROPERTY,
evt14 -> onlySpectrumMainPanel.updateSpectrum(currentSpectrum));
break;
}
spectrumShowJPanel.revalidate();
spectrumShowJPanel.repaint();
}
/**
* Return normal
* @param evt Mouse click event
*/
private void psmJTableMouseExited(MouseEvent evt) {
this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
/**
* Update spectrum according to the select psmKey
* @param evt Mouse click event
*/
private void psmJTableMouseReleased(MouseEvent evt) {
psmJTable.requestFocus();
int row = psmJTable.getSelectedRow();
int column = psmJTable.getSelectedColumn();
if (row != -1) {
this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
Spectrum selectedSpectrum = currentPeptideItemList.get(row).getSpectrum();
Number[] mzArray = selectedSpectrum.getMzNumberArray();
Number[] intentArray = selectedSpectrum.getIntentArray();
HashMap<Double, Peak> peakMap = new HashMap<>();
for (int i = 0; i<mzArray.length; i++){
Peak peak = new Peak(mzArray[i].doubleValue(), intentArray[i].doubleValue());
peakMap.put(mzArray[i].doubleValue(), peak);
}
ArrayList<Charge> chargeArrayList = new ArrayList<>();
chargeArrayList.add(currentTableMatchList.get(row).getBestPeptideAssumption().getIdentificationCharge());
Precursor precursor = new Precursor(-1.0, currentMz.get(row), chargeArrayList);
MSnSpectrum mSnSpectrum = new MSnSpectrum(2, precursor, String.valueOf(selectedSpectrum.getId()), peakMap, "");
selectedPSMKey = currentTablePSMKeyList.get(row);
updateSpectrum(mSnSpectrum, currentTableMatchList.get(row));
this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
}
/**
* Update spectrum according to the select psmKey
* @param evt Key event
*/
private void psmJTableKeyReleased(KeyEvent evt) {
psmJTable.requestFocus();
if (evt == null || evt.getKeyCode() == KeyEvent.VK_UP || evt.getKeyCode() == KeyEvent.VK_DOWN
|| evt.getKeyCode() == KeyEvent.VK_PAGE_UP || evt.getKeyCode() == KeyEvent.VK_PAGE_DOWN) {
final int row = psmJTable.getSelectedRow();
if (row != -1) {
Spectrum selectedSpectrum = currentPeptideItemList.get(row).getSpectrum();
Number[] mzArray = selectedSpectrum.getMzNumberArray();
Number[] intentArray = selectedSpectrum.getIntentArray();
HashMap<Double, Peak> peakMap = new HashMap<>();
for (int i = 0; i<mzArray.length; i++){
Peak peak = new Peak(mzArray[i].doubleValue(), intentArray[i].doubleValue());
peakMap.put(mzArray[i].doubleValue(), peak);
}
ArrayList<Charge> chargeArrayList = new ArrayList<>();
chargeArrayList.add(currentTableMatchList.get(row).getBestPeptideAssumption().getIdentificationCharge());
Precursor precursor = new Precursor(-1.0, currentMz.get(row), chargeArrayList);
MSnSpectrum mSnSpectrum = new MSnSpectrum(2, precursor, String.valueOf(selectedSpectrum.getId()), peakMap, "");
selectedPSMKey = currentTablePSMKeyList.get(row);
updateSpectrum(mSnSpectrum, currentTableMatchList.get(row));
}
}
}
/**
* Return normal
* @param evt Mouse click event
*/
private void spectrumJTableMouseExited(MouseEvent evt) {
this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
/**
* spectrumJTableMouseReleased
* @param evt Mouse click event
*/
private void spectrumJTableMouseReleased(MouseEvent evt){
spectrumJTable.requestFocus();
int row = spectrumJTable.getSelectedRow();
int column = spectrumJTable.getSelectedColumn();
if (row != -1) {
this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
String id =String.valueOf(spectrumJTable.getValueAt(row, 0));
Spectrum selectedSpectrum = currentPrideXmlReader.getSpectrumById(id);
Number[] mzArray = selectedSpectrum.getMzNumberArray();
Number[] intentArray = selectedSpectrum.getIntentArray();
HashMap<Double, Peak> peakMap = new HashMap<>();
for (int i = 0; i<mzArray.length; i++){
Peak peak = new Peak(mzArray[i].doubleValue(), intentArray[i].doubleValue());
peakMap.put(mzArray[i].doubleValue(), peak);
}
ArrayList<Charge> chargeArrayList = new ArrayList<>();
chargeArrayList.add(new Charge(+1, (Integer) spectrumJTable.getValueAt(row, 2)));
Precursor precursor = new Precursor(-1.0, (Double) spectrumJTable.getValueAt(row, 3), chargeArrayList);
currentSpectrum = new MSnSpectrum(2, precursor, id, peakMap, "");
selectedPSMKey = String.valueOf(row);
onlySpectrumMainPanel.updateSpectrum(currentSpectrum);
spectrumShowJPanel.revalidate();
spectrumShowJPanel.repaint();
}
this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
/**
* spectrumJTableKeyReleased
* @param evt Mouse click event
*/
private void spectrumJTableKeyReleased(KeyEvent evt){
spectrumJTable.requestFocus();
if (evt == null || evt.getKeyCode() == KeyEvent.VK_UP || evt.getKeyCode() == KeyEvent.VK_DOWN
|| evt.getKeyCode() == KeyEvent.VK_PAGE_UP || evt.getKeyCode() == KeyEvent.VK_PAGE_DOWN) {
final int row = spectrumJTable.getSelectedRow();
if (row != -1) {
this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
String id =String.valueOf(spectrumJTable.getValueAt(row, 0));
Spectrum selectedSpectrum = currentPrideXmlReader.getSpectrumById(id);
Number[] mzArray = selectedSpectrum.getMzNumberArray();
Number[] intentArray = selectedSpectrum.getIntentArray();
HashMap<Double, Peak> peakMap = new HashMap<>();
for (int i = 0; i<mzArray.length; i++){
Peak peak = new Peak(mzArray[i].doubleValue(), intentArray[i].doubleValue());
peakMap.put(mzArray[i].doubleValue(), peak);
}
ArrayList<Charge> chargeArrayList = new ArrayList<>();
chargeArrayList.add(new Charge(+1, (Integer) spectrumJTable.getValueAt(row, 2)));
Precursor precursor = new Precursor(-1.0, (Double) spectrumJTable.getValueAt(row, 3), chargeArrayList);
currentSpectrum = new MSnSpectrum(2, precursor, id, peakMap, "");
selectedPSMKey = String.valueOf(row);
onlySpectrumMainPanel.updateSpectrum(currentSpectrum);
}
}
}
/**
* Update spectrum
* @param mSnSpectrum MSN Spectrum
* @param spectrumMatch Spectrum match
*/
private void updateSpectrum(MSnSpectrum mSnSpectrum, SpectrumMatch spectrumMatch){
spectrumShowJPanel.setBorder(BorderFactory.createTitledBorder(spectrumMatch.getBestPeptideAssumption().getPeptide().getSequence()));
spectrumMainPanel.updateSpectrum(spectrumMatch.getBestPeptideAssumption(), mSnSpectrum, selectedPSMKey);
spectrumShowJPanel.revalidate();
spectrumShowJPanel.repaint();
}
/**
* Update tree
* @param prideXmlReader PrideXML reader
*/
public void updateTree(PrideXmlReader prideXmlReader){
if(!titleToPrideXmlReader.containsValue(prideXmlReader)){
treeJPanel.removeAll();
String title = prideXmlReader.getExpTitle();
titleToPrideXmlReader.put(title, prideXmlReader);
DefaultMutableTreeNode root = new DefaultMutableTreeNode("Files");
DefaultTreeModel treeModel = new DefaultTreeModel(root);
List<String> identificationList;
for(String eachTtitle : titleToPrideXmlReader.keySet()){
PrideXmlReader prideXmlReaderInList = titleToPrideXmlReader.get(eachTtitle);
identificationList = prideXmlReaderInList.getIdentIds();
DefaultMutableTreeNode prideFileRoot = new DefaultMutableTreeNode(eachTtitle + "( "+identificationList.size()+" )");
treeModel.insertNodeInto(prideFileRoot, root, root.getChildCount());
ArrayList<String> proteinAccessionList = new ArrayList<>();
for(String identification : identificationList){
Identification identificationValue = prideXmlReaderInList.getIdentById(identification);
proteinAccessionList.add(identificationValue.getAccession() +"( "+ identificationValue.getPeptideItem().size()+" )");
accessionToId.put(identificationValue.getAccession(), identification);
}
Collections.sort(proteinAccessionList);
for (String proteinName : proteinAccessionList){
DefaultMutableTreeNode proteinNode = new DefaultMutableTreeNode(proteinName);
treeModel.insertNodeInto(proteinNode, prideFileRoot, prideFileRoot.getChildCount());
}
}
JScrollPane jScrollPane;
JTree tree = new JTree(treeModel);
tree.setOpaque(true);
tree.setBackground(Color.white);
tree.getSelectionModel().setSelectionMode(
TreeSelectionModel.SINGLE_TREE_SELECTION);
tree.addTreeSelectionListener(this::valueChanged);
tree.setSelectionInterval(1,1);
jScrollPane = new JScrollPane(tree);
jScrollPane.setOpaque(false);
jScrollPane.setBackground(Color.white);
GroupLayout treeJPanelLayout = new GroupLayout(treeJPanel);
treeJPanel.setLayout(treeJPanelLayout);
treeJPanelLayout.setHorizontalGroup(
treeJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(jScrollPane, GroupLayout.DEFAULT_SIZE, 200, Short.MAX_VALUE)
);
treeJPanelLayout.setVerticalGroup(
treeJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(jScrollPane, GroupLayout.DEFAULT_SIZE, 500, Short.MAX_VALUE)
);
allJSplitPane.setDividerLocation(0.2);
tabelAndChartJSplit.setDividerLocation(0.4);
treeJPanel.revalidate();
treeJPanel.repaint();
}
}
/**
* Tree valueChanged
* @param evt TreeSelectionEvent
*/
private void valueChanged(TreeSelectionEvent evt) {
JTree tree = (JTree)evt.getSource();
DefaultMutableTreeNode selectionNode = (DefaultMutableTreeNode)tree.getLastSelectedPathComponent();
TreeNode parentNode = selectionNode.getParent();
String nodeName = selectionNode.toString().split("\\(")[0];
if(titleToPrideXmlReader.containsKey(nodeName)){
currentPrideXmlReader = titleToPrideXmlReader.get(nodeName);
currentProtein = selectionNode.getFirstChild().toString().split("\\(")[0];
currentFileCount = parentNode.getIndex(selectionNode) + 1;
currentProteinCount = 1;
updatePSMJTable();
updateDetails();
updateSpectrumTable();
} else if(!nodeName.equals("Files")){
if(currentPrideXmlReader != titleToPrideXmlReader.get(parentNode.toString().split("\\(")[0])){
currentPrideXmlReader = titleToPrideXmlReader.get(parentNode.toString().split("\\(")[0]);
updateDetails();
updateSpectrumTable();
}
currentProtein = nodeName;
TreeNode grandNode = parentNode.getParent();
currentFileCount = grandNode.getIndex(parentNode) + 1;
currentProteinCount = parentNode.getIndex(selectionNode) + 1;
updatePSMJTable();
}
tree.requestFocus();
}
/**
* updatePSMJTable
*/
private void updatePSMJTable(){
currentPeptideList.clear();
currentTableMatchList.clear();
currentMz.clear();
currentTablePSMKeyList.clear();
String id = accessionToId.get(currentProtein);
Identification gelFreeIdentification = currentPrideXmlReader.getIdentById(id);
String database = gelFreeIdentification.getDatabase();
Double score = gelFreeIdentification.getScore();
String searchEngine = gelFreeIdentification.getSearchEngine();
psmJPanel.setBorder(new TitledBorder("PSM Table ("+currentProtein+" in "+database + " Searched by "+searchEngine + " Score: "+score + ")"));
currentPeptideItemList = gelFreeIdentification.getPeptideItem();
ArrayList<String> additionPara = new ArrayList<>();
ArrayList<HashMap<String, String>> additionalParaMapList = new ArrayList<>();
String peptideSequence;
List<ModificationItem> modificationItemList;
List<CvParam> cvParamList;
List<CvParam> precursorCvParamList;
HashMap<String, String> eachAdditionalPara;
ArrayList<ModificationMatch> utilitiesModifications;
PeptideAssumption peptideAssumption;
Peptide peptide;
SpectrumMatch spectrumMatch;
Spectrum spectrum;
Integer psmCount = 0;
ArrayList<String> residues = new ArrayList<>();
for (PeptideItem peptideItem : currentPeptideItemList){
psmCount ++;
peptideSequence = peptideItem.getSequence();
modificationItemList = peptideItem.getModificationItem();
utilitiesModifications = new ArrayList<>();
for (ModificationItem modificationItem : modificationItemList){
Integer location = modificationItem.getModLocation().intValue();
String accession = modificationItem.getModAccession();
String nameFromPride = "";
String modificationName = null;
List<CvParam> cvParams = modificationItem.getAdditional().getCvParam();
for (CvParam cvParam : cvParams){
if (cvParam.getName() != null) {
nameFromPride = cvParam.getName();
} else {
nameFromPride = accession;
}
}
Double monoMassDelta = Double.valueOf(modificationItem.getModMonoDelta().get(0));
HashMap<Double, String > massModification;
if(location == 0){
modificationName = nameFromPride + " of N-term";
if (!ptmFactory.containsPTM(modificationName)){
PTM ptm = new PTM(PTM.MODNP, modificationName, monoMassDelta, null);
ptm.setShortName(nameFromPride);
ptmFactory.addUserPTM(ptm);
}
location = 1;
}else if(location == peptideSequence.length() + 1){
modificationName = nameFromPride + " of C-term";
if (!ptmFactory.containsPTM(modificationName)){
PTM ptm = new PTM(PTM.MODCP, modificationName, monoMassDelta, null);
ptm.setShortName(nameFromPride);
ptmFactory.addUserPTM(ptm);
}
location = peptideSequence.length();
}else {
residues = new ArrayList<>();
String aa = String.valueOf(peptideSequence.charAt(location - 1));
residues.add(aa);
modificationName = nameFromPride + " of " + aa;
if (!ptmFactory.containsPTM(modificationName)){
PTM ptm = new PTM(PTM.MODAA, modificationName, monoMassDelta, residues);
ptm.setShortName(nameFromPride);
ptmFactory.addUserPTM(ptm);
}
}
utilitiesModifications.add(new ModificationMatch(modificationName, true, location));
}
peptide = new Peptide(peptideSequence, utilitiesModifications);
spectrumMatch = new SpectrumMatch();
spectrum = peptideItem.getSpectrum();
precursorCvParamList = spectrum.getSpectrumDesc().getPrecursorList().getPrecursor().get(0).getIonSelection().getCvParam();
Integer charge = -1;
Double mz = 0.0;
for (CvParam cvParam : precursorCvParamList){
if (cvParam.getAccession().contains("1000041")){
charge = Integer.valueOf(cvParam.getValue());
} else if (cvParam.getAccession().contains("1000744")){
mz = Double.valueOf(cvParam.getValue());
} else if (cvParam.getAccession().contains("1000040")){
mz = Double.valueOf(cvParam.getValue());
}
}
currentMz.add(mz);
peptideAssumption = new PeptideAssumption(peptide, 1, 0, new Charge(+1, charge), 0.0, "");
spectrumMatch.setBestPeptideAssumption(peptideAssumption);
currentTableMatchList.add(spectrumMatch);
currentPeptideList.add(peptide);
currentTablePSMKeyList.add(String.valueOf(currentFileCount)+String.valueOf(currentProteinCount)+String.valueOf(psmCount));
cvParamList = peptideItem.getAdditional().getCvParam();
eachAdditionalPara = new HashMap<>();
for (CvParam cvParam : cvParamList){
if (!additionPara.contains(cvParam.getName())){
additionPara.add(cvParam.getName());
}
eachAdditionalPara.put(cvParam.getName(), cvParam.getValue());
}
additionalParaMapList.add(eachAdditionalPara);
}
setUpTableHeaderToolTips();
psmJTableToolTips.addAll(additionPara);
PSMTableMode psmTableMode = new PSMTableMode(currentPeptideList, additionPara, additionalParaMapList, currentPeptideItemList, searchParameters, currentFileCount, currentProteinCount);
psmJTable.setModel(psmTableMode);
psmJPanel.repaint();
psmJTable.addRowSelectionInterval(0,0);
psmJTableMouseReleased(null);
}
/**
* Update spectrum table
*/
private void updateSpectrumTable(){
List<String> spectrumIDs = currentPrideXmlReader.getSpectrumIds();
spectrumTableJPanel.setBorder(BorderFactory.createTitledBorder("Spectrum Table (" + spectrumIDs.size() + ")"));
SpectrumTableModel spectrumTableModel = new SpectrumTableModel(currentPrideXmlReader, spectrumIDs);
spectrumJTable.setModel(spectrumTableModel);
spectrumTableJPanel.repaint();
spectrumJTable.addRowSelectionInterval(0,0);
spectrumJTableMouseReleased(null);
}
/**
* Update file details
*/
private void updateDetails(){
ArrayList<String> detailsList = new ArrayList<>();
if (currentPrideXmlReader.getExpTitle() != null){
detailsList.add("Exp Title /t/" + currentPrideXmlReader.getExpTitle());
}
if(currentPrideXmlReader.getExpShortLabel() != null ){
detailsList.add("Short Label /t/" + currentPrideXmlReader.getExpShortLabel());
}
Protocol currentProtocol = currentPrideXmlReader.getProtocol();
if (currentProtocol.getProtocolName() != null){
detailsList.add("Protocol Name /t/" + currentProtocol.getProtocolName());
}
if (currentProtocol.getProtocolSteps() != null){
if (currentProtocol.getProtocolSteps().getStepDescription() != null){
List<Param> protocolSteps = currentProtocol.getProtocolSteps().getStepDescription();
for (Param param : protocolSteps){
for(CvParam cvParam : param.getCvParam()){
detailsList.add(cvParam.getName() + "/t/" + cvParam.getValue());
}
}
}
}
if (currentPrideXmlReader.getAdmin() != null){
Admin currentAdmin = currentPrideXmlReader.getAdmin();
detailsList.add("Sample Name /t/" + currentAdmin.getSampleName());
if (currentAdmin.getSampleDescription() != null){
for (CvParam cvParam : currentAdmin.getSampleDescription().getCvParam()){
detailsList.add(cvParam.getCvLabel() + "/t/" + cvParam.getName());
}
}
if (currentAdmin.getContact() != null){
for (Contact contact : currentAdmin.getContact()){
if(contact.getName() != null){
detailsList.add("Name /t/" + contact.getName());
}
if(contact.getInstitution() != null){
detailsList.add("Institution /t/" + contact.getInstitution());
}
if(contact.getContactInfo() != null){
detailsList.add("Contact Info /t/" + contact.getContactInfo());
}
}
}
}
if (currentPrideXmlReader.getInstrument() !=null){
Instrument instrument = currentPrideXmlReader.getInstrument();
detailsList.add("Instrument Name /t/" + instrument.getInstrumentName());
if (instrument.getSource() != null){
for(CvParam cvParam : instrument.getSource().getCvParam()){
detailsList.add("Source /t/" + cvParam.getName());
}
}
if (instrument.getAnalyzerList() != null) {
Integer count = 1;
if (instrument.getAnalyzerList().getAnalyzer() != null) {
for (Param param : instrument.getAnalyzerList().getAnalyzer()) {
for (CvParam cvParam : param.getCvParam()) {
detailsList.add("Analyzer" + count + "/t/" + cvParam.getName());
}
count++;
}
}
}
if (instrument.getDetector() != null) {
for (CvParam cvParam : instrument.getDetector().getCvParam()) {
detailsList.add("Detector /t/ "+ cvParam.getName());
}
}
}
if (currentPrideXmlReader.getDataProcessing() != null){
DataProcessing currentDataProcessing = currentPrideXmlReader.getDataProcessing();
if (currentDataProcessing.getSoftware() != null){
detailsList.add("Software /t/ " + currentDataProcessing.getSoftware().getName() + "-"+currentDataProcessing.getSoftware().getVersion());
}
if (currentDataProcessing.getProcessingMethod() != null){
for(CvParam cvParam : currentDataProcessing.getProcessingMethod().getCvParam()){
detailsList.add("Processing Method: " + cvParam.getName() + "/t/" + cvParam.getValue());
}
}
}
if (currentPrideXmlReader.getAdditionalParams() != null){
for(CvParam cvParam : currentPrideXmlReader.getAdditionalParams().getCvParam()){
detailsList.add(cvParam.getName() + "/t/" + cvParam.getValue());
}
}
HashMap<String, ArrayList<String>> selectedOri = new HashMap<>();
selectedOri.put(currentPrideXmlReader.getExpTitle(), detailsList);
infoPanel.updateInfo(selectedOri);
}
/**
* Get Modification mass map
* @return HashMap
*/
public HashMap<String,HashMap<Double, String >> getModificationMass(){
HashMap<String,HashMap<Double, String > > modificationMass = new HashMap<>();
ArrayList<String> orderedModifications = ptmFactory.getPTMs();
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).put(ptmFactory.getPTM(modificationName).getMass(), modificationName);
}else {
HashMap<Double, String> singleModi = new HashMap<>();
singleModi.put(ptmFactory.getPTM(modificationName).getMass(), modificationName);
modificationMass.put(aminoAcidName, singleModi);
}
}
return modificationMass;
}
/**
* PSM table model
*/
public class PSMTableMode extends DefaultTableModel{
/**
* Current peptide list
*/
private ArrayList<Peptide> currentPeptideList;
/**
* Additional parameters
*/
private ArrayList<String> additionalPara;
/**
* Search parameters
*/
private SearchParameters searchParameters;
/**
* Peptide item list
*/
private java.util.List<PeptideItem> peptideItemList;
/**
* Current file count
*/
private String currentFileCount;
/**
* Current protein count
*/
private String currentProteinCount;
/**
* Additional parameters list
*/
private ArrayList<HashMap<String, String>> additionalParaMapList;
/**
* Constructor
* @param currentPeptideList Current peptide list
* @param additionalPara Additional parameters list
* @param additionalParaMapList Additional parameters map
* @param peptideItemList Peptide item list
* @param searchParameters Search parameters
* @param currentFileCount Current file count
* @param currentProteinCount Current protein count
*/
public PSMTableMode(ArrayList<Peptide> currentPeptideList, ArrayList<String> additionalPara, ArrayList<HashMap<String, String>> additionalParaMapList,
java.util.List<PeptideItem> peptideItemList, SearchParameters searchParameters, Integer currentFileCount, Integer currentProteinCount){
this.currentPeptideList = currentPeptideList;
this.additionalPara = additionalPara;
this.searchParameters = searchParameters;
this.peptideItemList = peptideItemList;
this.currentFileCount = String.valueOf(currentFileCount);
this.currentProteinCount = String.valueOf(currentProteinCount);
this.additionalParaMapList = additionalParaMapList;
}
@Override
public int getRowCount() {
if (currentPeptideList != null) {
return currentPeptideList.size();
} else {
return 0;
}
}
@Override
public int getColumnCount() {
if(additionalPara != null) {
return additionalPara.size()+7;
} else {
return 7;
}
}
@Override
public String getColumnName(int column) {
if(column == 0){
return "Key";
}else if(column == 1){
return "Sequence";
}else if(column == 2){
return "Rf Spectrum";
}else if(column == 3){
return "Charge";
}else if(column == 4){
return "m/z";
}else if(column == 5){
return "Rt (min)";
}else if(column == 6){
return "Comments";
}
for(int index = 0; index < additionalPara.size(); index++){
int newColumn = index + 7;
if(column == newColumn){
return additionalPara.get(index);
}
}
return "";
}
@Override
public Object getValueAt(int row, int column) {
try {
if(row < currentPeptideList.size()){
Peptide peptide = currentPeptideList.get(row);
PeptideItem peptideItem = peptideItemList.get(row);
Spectrum spectrum = peptideItem.getSpectrum();
List<CvParam> cvParamList = spectrum.getSpectrumDesc().getPrecursorList().getPrecursor().get(0).getIonSelection().getCvParam();
HashMap<String, String> eachRowAddition = additionalParaMapList.get(row);
if (column == 0){
return currentFileCount+currentProteinCount +String.valueOf(row+1);
}
if (column == 1){
return peptide.getTaggedModifiedSequence(searchParameters.getPtmSettings(), true, true, false, false);
}
if (column == 2){
return spectrum.getId();
}
if (column == 3){
Integer charge = -1;
for (CvParam cvParam : cvParamList){
if (cvParam.getAccession().contains("1000041")){
charge = Integer.valueOf(cvParam.getValue());
}
}
return charge;
}
if (column == 4){
Double mz = -1.0;
for (CvParam cvParam : cvParamList){
if (cvParam.getAccession().contains("1000744")){
mz = Double.valueOf(cvParam.getValue());
} else if (cvParam.getAccession().contains("1000040")){
mz = Double.valueOf(cvParam.getValue());
}
}
return mz;
}
if (column == 5){
return -1;
}
if (column == 6){
List<String> comments = spectrum.getSpectrumDesc().getComments();
if (comments.size() != 0){
return comments.get(0);
} else {
return "";
}
}
for(int index = 0; index < additionalPara.size(); index++){
int newColumn = index + 7;
if(column == newColumn){
return eachRowAddition.get(additionalPara.get(index));
}
}
} else {
return "";
}
} catch (Exception e){
e.printStackTrace();
return "";
}
return "";
}
@Override
public boolean isCellEditable(int rowIndex, int columnIndex) {
return false;
}
@Override
public Class getColumnClass(int columnIndex) {
for (int i = 0; i < getRowCount(); i++) {
if (getValueAt(i, columnIndex) != null) {
return getValueAt(i, columnIndex).getClass();
}
}
return String.class;
}
}
/**
* Spectrum table model
*/
public class SpectrumTableModel extends DefaultTableModel{
/**
* PrideXML reader
*/
private PrideXmlReader prideXmlReader;
/**
* Spectrum ID list
*/
private List<String> spectrumIDs;
/**
* Constructor
* @param prideXmlReader PrideXML reader
* @param spectrumIDs Spectrum ID lsit
*/
public SpectrumTableModel(PrideXmlReader prideXmlReader, List<String> spectrumIDs){
this.spectrumIDs = spectrumIDs;
this.prideXmlReader = prideXmlReader;
}
@Override
public int getRowCount() {
if (spectrumIDs != null) {
return spectrumIDs.size();
} else {
return 0;
}
}
@Override
public int getColumnCount() {
return 9;
}
@Override
public String getColumnName(int column) {
if(column == 0){
return "Spectrum ID";
}else if(column == 1){
return "MS Level";
}else if(column == 2){
return "Precursor Charge";
}else if(column == 3){
return "Precursor m/z";
}else if(column == 4){
return "mzRange start";
}else if(column == 5){
return "mzRange stop";
}else if(column == 6){
return "Peaks Num";
}else if(column == 7) {
return "Intensity Sum";
}else if(column == 8) {
return "Identified";
}
return "";
}
@Override
public Object getValueAt(int row, int column) {
try {
if(row < spectrumIDs.size()){
String spectrumID = spectrumIDs.get(row);
Spectrum spectrum = prideXmlReader.getSpectrumById(spectrumID);
SpectrumDesc spectrumDesc = spectrum.getSpectrumDesc();
SpectrumInstrument spectrumInstrument = spectrumDesc.getSpectrumSettings().getSpectrumInstrument();
uk.ac.ebi.pride.jaxb.model.Precursor precursor = spectrumDesc.getPrecursorList().getPrecursor().get(0);
List<CvParam> ionSelection = precursor.getIonSelection().getCvParam();
Number[] intensityArray = spectrum.getIntentArray();
if (column == 0){
return spectrum.getId();
}
if (column == 1){
return spectrumInstrument.getMsLevel();
}
if (column == 2){
Integer charge = -1;
for (CvParam cvParam : ionSelection){
if (cvParam.getAccession().contains("1000041")){
charge = Integer.valueOf(cvParam.getValue());
}
}
return charge;
}
if (column == 3){
Double mz = -1.0;
for (CvParam cvParam : ionSelection){
if (cvParam.getAccession().contains("1000744")){
mz = Double.valueOf(cvParam.getValue());
} else if (cvParam.getAccession().contains("1000040")){
mz = Double.valueOf(cvParam.getValue());
}
}
return mz;
}
if (column == 4){
return spectrumInstrument.getMzRangeStart();
}
if (column == 5){
return spectrumInstrument.getMzRangeStop();
}
if (column == 6){
return spectrum.getMzArrayBinary().getData().getLength();
}
if (column == 7){
Double sum = 0.0;
for(Number number : intensityArray){
sum += number.doubleValue();
}
return sum;
}
if (column == 8){
List<String> comments = spectrum.getSpectrumDesc().getComments();
if (comments.size() != 0){
return comments.get(0);
} else {
return "";
}
}
} else {
return "";
}
} catch (Exception e){
e.printStackTrace();
return "";
}
return "";
}
@Override
public boolean isCellEditable(int rowIndex, int columnIndex) {
return false;
}
@Override
public Class getColumnClass(int columnIndex) {
for (int i = 0; i < getRowCount(); i++) {
if (getValueAt(i, columnIndex) != null) {
return getValueAt(i, columnIndex).getClass();
}
}
return String.class;
}
}
}
