public void clearData(boolean clearDatabaseFolder) {
projectDetails = null;
spectrumAnnotator = new SpectrumAnnotator();
try {
spectrumFactory.closeFiles();
} catch (Exception e) {
e.printStackTrace();
}
try {
sequenceFactory.closeFile();
} catch (Exception e) {
e.printStackTrace();
}
try {
GOFactory.getInstance().closeFiles();
} catch (Exception e) {
e.printStackTrace();
}
try {
spectrumFactory.clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
try {
sequenceFactory.clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
try {
GOFactory.getInstance().clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
identifiedModifications = null;
if (clearDatabaseFolder) {
clearDatabaseFolder();
}
resetFeatureGenerator();
// set up the tabs/panels
currentPSFile = null;
}
/**
* Returns the desired spectrum.
*
* @param spectrumKey the key of the spectrum
* @return the desired spectrum
*/
public MSnSpectrum getSpectrum(String spectrumKey) {
String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
String spectrumTitle = Spectrum.getSpectrumTitle(spectrumKey);
try {
return (MSnSpectrum) spectrumFactory.getSpectrum(spectrumFile, spectrumTitle);
} catch (Exception e) {
System.out.println(e.getMessage());
return null;
}
}
/**
* A Jump To panel for use in the menu bar in the main frame.
*
* @author Marc Vaudel
* @author Harald Barsnes
*/
public class JumpToPanel extends javax.swing.JPanel {
/** Enum of the types of data to jump to. */
public enum JumpType {
proteinAndPeptides,
spectrum
}
/** The type of data to jump to in that panel. */
private JumpType jumpType = JumpType.proteinAndPeptides;
/** Instance of the main GUI class. */
private PeptideShakerGUI peptideShakerGUI;
/** Items matching the criterion for each type. */
private HashMap<JumpType, ArrayList<String>> possibilities =
new HashMap<JumpType, ArrayList<String>>();
/** Currently selected item. */
private HashMap<JumpType, Integer> currentSelection = new HashMap<JumpType, Integer>();
/** The text to display by default. */
private HashMap<JumpType, String> lastInput = new HashMap<JumpType, String>();
/** The text to display by default. */
private HashMap<JumpType, String> lastLabel = new HashMap<JumpType, String>();
/** Instance of the sequence factory. */
private SequenceFactory sequenceFactory = SequenceFactory.getInstance();
/** The text to display by default. */
private HashMap<JumpType, String> welcomeText;
/** The spectrum factory. */
private SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
/** The spectrum file inspected when jumping to spectra. */
private String spectrumfile;
/** Counts the number of times the users has pressed a key on the keyboard in the search field. */
private int keyPressedCounter = 0;
/** The time to wait between keys typed before updating the search. */
private int waitingTime = 1000;
/** Type of item selected. */
private enum Type {
PROTEIN,
PEPTIDE,
SPECTRUM
}
/** Type of each possible item. */
private HashMap<JumpType, ArrayList<Type>> types = new HashMap<JumpType, ArrayList<Type>>();
/**
* Creates a new JumpToPanel.
*
* @param peptideShakerGUI the parent
*/
public JumpToPanel(PeptideShakerGUI peptideShakerGUI) {
initComponents();
this.peptideShakerGUI = peptideShakerGUI;
welcomeText = new HashMap<JumpType, String>();
welcomeText.put(JumpType.proteinAndPeptides, "(protein or peptide)");
welcomeText.put(JumpType.spectrum, "(title, m/z or RT)");
inputTxt.setText(welcomeText.get(jumpType));
indexLabel.setText("");
previousButton.setEnabled(false);
nextButton.setEnabled(false);
}
/** Move the focus to the Jump To text field and select all the content. */
public void selectTextField() {
inputTxt.requestFocus();
inputTxt.selectAll();
}
/**
* Set the color for the hits.
*
* @param color the color
*/
public void setColor(Color color) {
indexLabel.setForeground(color);
}
/** Updates the item selection in the selected tab. */
public void updateSelectionInTab() {
indexLabel.setForeground(Color.BLACK);
if (types.get(jumpType).get(currentSelection.get(jumpType)) == Type.PROTEIN) {
peptideShakerGUI.setSelectedItems(
possibilities.get(jumpType).get(currentSelection.get(jumpType)),
PeptideShakerGUI.NO_SELECTION,
PeptideShakerGUI.NO_SELECTION);
peptideShakerGUI.updateSelectionInCurrentTab();
} else if (types.get(jumpType).get(currentSelection.get(jumpType)) == Type.PEPTIDE) {
peptideShakerGUI.setSelectedItems(
PeptideShakerGUI.NO_SELECTION,
possibilities.get(jumpType).get(currentSelection.get(jumpType)),
PeptideShakerGUI.NO_SELECTION);
if (peptideShakerGUI.getSelectedTab() == PeptideShakerGUI.MODIFICATIONS_TAB_INDEX
&& !peptideShakerGUI
.getDisplayedPeptides()
.contains(possibilities.get(jumpType).get(currentSelection.get(jumpType)))) {
// warn the user that the current selection is not in the tab
indexLabel.setForeground(Color.RED);
} else {
peptideShakerGUI.updateSelectionInCurrentTab();
}
} else {
peptideShakerGUI.setSelectedItems(
PeptideShakerGUI.NO_SELECTION,
PeptideShakerGUI.NO_SELECTION,
possibilities.get(jumpType).get(currentSelection.get(jumpType)));
peptideShakerGUI.updateSelectionInCurrentTab();
}
String label =
"("
+ (currentSelection.get(jumpType) + 1)
+ " of "
+ possibilities.get(jumpType).size()
+ ")";
indexLabel.setText(label);
lastLabel.put(jumpType, label);
}
/**
* Returns a list of descriptions corresponding to every item matching the search.
*
* @return a list of descriptions
* @throws SQLException thrown if an SQLException occurs
* @throws ClassNotFoundException thrown if a ClassNotFoundException occurs
* @throws IOException thrown if an IOException occurs
* @throws InterruptedException thrown if an InterruptedException occurs
*/
public ArrayList<String> getPossibilitiesDescriptions()
throws SQLException, ClassNotFoundException, IOException, InterruptedException {
Identification identification = peptideShakerGUI.getIdentification();
// Some necessary pre-caching
ArrayList<Type> typeList = types.get(jumpType);
ArrayList<String> keys = possibilities.get(jumpType),
proteinKeys = new ArrayList<String>(),
peptideKeys = new ArrayList<String>();
for (int i = 0; i < keys.size(); i++) {
String key = keys.get(i);
if (typeList.get(i) == Type.PROTEIN) {
proteinKeys.add(key);
} else if (typeList.get(i) == Type.PEPTIDE) {
peptideKeys.add(key);
}
}
if (!proteinKeys.isEmpty()) {
identification.loadProteinMatches(proteinKeys, null, false);
}
if (!peptideKeys.isEmpty()) {
identification.loadPeptideMatches(peptideKeys, null, false);
}
ArrayList<String> descriptions = new ArrayList<String>();
for (int i = 0; i < keys.size(); i++) {
String key = keys.get(i);
Type type = typeList.get(i);
String description = getItemDescription(key, type);
descriptions.add(description);
}
return descriptions;
}
/**
* Returns the description of an item.
*
* @param key the key of the item
* @param itemType the type of the item
* @return the description of an item
* @throws SQLException thrown if an SQLException occurs
* @throws ClassNotFoundException thrown if a ClassNotFoundException occurs
* @throws IOException thrown if an IOException occurs
* @throws InterruptedException thrown if an InterruptedException occurs
*/
private String getItemDescription(String key, Type itemType)
throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException,
InterruptedException {
Identification identification = peptideShakerGUI.getIdentification();
switch (itemType) {
case PROTEIN:
ProteinMatch proteinMatch = identification.getProteinMatch(key);
String mainMatch = proteinMatch.getMainMatch();
String description = sequenceFactory.getHeader(mainMatch).getSimpleProteinDescription();
String result = mainMatch;
for (String accession : ProteinMatch.getAccessions(key)) {
if (!accession.equals(mainMatch)) {
if (!result.equals(mainMatch)) {
result += ", ";
}
result += accession;
}
}
result += " - " + description;
return result;
case PEPTIDE:
PeptideMatch peptideMatch = identification.getPeptideMatch(key);
return peptideShakerGUI
.getDisplayFeaturesGenerator()
.getTaggedPeptideSequence(peptideMatch, true, true, true);
case SPECTRUM:
return Spectrum.getSpectrumTitle(key) + " (" + Spectrum.getSpectrumFile(key) + ")";
default:
return "Unknown";
}
}
/**
* Returns the index of the selected item.
*
* @return the index of the selected item
*/
public int getIndexOfSelectedItem() {
return currentSelection.get(jumpType);
}
/**
* Sets the index of the selected item. Note: this does not update the selection in tab and the
* GUI (see updateSelectionInTab()).
*
* @param itemIndex the item index
*/
public void setSelectedItem(int itemIndex) {
currentSelection.put(jumpType, itemIndex);
}
/**
* This method is called from within the constructor to initialize the form. WARNING: Do NOT
* modify this code. The content of this method is always regenerated by the Form Editor.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
findJLabel = new javax.swing.JLabel();
inputTxt = new javax.swing.JTextField();
previousButton = new javax.swing.JButton();
nextButton = new javax.swing.JButton();
indexLabel = new javax.swing.JLabel();
setOpaque(false);
findJLabel.setText("Find");
inputTxt.setForeground(new java.awt.Color(204, 204, 204));
inputTxt.setHorizontalAlignment(javax.swing.JTextField.CENTER);
inputTxt.setText("(peptide or protein)");
inputTxt.setBorder(
javax.swing.BorderFactory.createLineBorder(new java.awt.Color(204, 204, 204)));
inputTxt.addMouseListener(
new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
inputTxtMouseReleased(evt);
}
});
inputTxt.addKeyListener(
new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
inputTxtKeyReleased(evt);
}
});
previousButton.setIcon(
new javax.swing.ImageIcon(getClass().getResource("/icons/previous_grey.png"))); // NOI18N
previousButton.setToolTipText("Previous");
previousButton.setBorder(null);
previousButton.setBorderPainted(false);
previousButton.setContentAreaFilled(false);
previousButton.setIconTextGap(0);
previousButton.setRolloverIcon(
new javax.swing.ImageIcon(getClass().getResource("/icons/previous.png"))); // NOI18N
previousButton.addMouseListener(
new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
previousButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
previousButtonMouseExited(evt);
}
});
previousButton.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
previousButtonActionPerformed(evt);
}
});
nextButton.setIcon(
new javax.swing.ImageIcon(getClass().getResource("/icons/next_grey.png"))); // NOI18N
nextButton.setToolTipText("Next");
nextButton.setBorderPainted(false);
nextButton.setContentAreaFilled(false);
nextButton.setRolloverIcon(
new javax.swing.ImageIcon(getClass().getResource("/icons/next.png"))); // NOI18N
nextButton.addMouseListener(
new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
nextButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
nextButtonMouseExited(evt);
}
});
nextButton.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
nextButtonActionPerformed(evt);
}
});
indexLabel.setFont(
indexLabel.getFont().deriveFont((indexLabel.getFont().getStyle() | java.awt.Font.ITALIC)));
indexLabel.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
indexLabel.setText(" ");
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
this.setLayout(layout);
layout.setHorizontalGroup(
layout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
layout
.createSequentialGroup()
.addContainerGap()
.addComponent(findJLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(
inputTxt,
javax.swing.GroupLayout.PREFERRED_SIZE,
205,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(
previousButton,
javax.swing.GroupLayout.PREFERRED_SIZE,
15,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(0, 0, 0)
.addComponent(
nextButton,
javax.swing.GroupLayout.PREFERRED_SIZE,
15,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(
indexLabel,
javax.swing.GroupLayout.PREFERRED_SIZE,
97,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap()));
layout.linkSize(
javax.swing.SwingConstants.HORIZONTAL,
new java.awt.Component[] {nextButton, previousButton});
layout.setVerticalGroup(
layout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
layout
.createSequentialGroup()
.addContainerGap()
.addGroup(
layout
.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(findJLabel)
.addComponent(
inputTxt,
javax.swing.GroupLayout.PREFERRED_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(indexLabel)
.addComponent(
previousButton,
javax.swing.GroupLayout.PREFERRED_SIZE,
15,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(
nextButton,
javax.swing.GroupLayout.PREFERRED_SIZE,
15,
javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap()));
} // </editor-fold>//GEN-END:initComponents
/**
* Update the jump to filter.
*
* @param evt the key event
*/
private void inputTxtKeyReleased(
java.awt.event.KeyEvent evt) { // GEN-FIRST:event_inputTxtKeyReleased
final KeyEvent event = evt;
keyPressedCounter++;
new Thread("FindThread") {
@Override
public synchronized void run() {
try {
wait(waitingTime);
} catch (InterruptedException e) {
e.printStackTrace();
}
try {
// see if the gui is to be updated or not
Identification identification = peptideShakerGUI.getIdentification();
if (identification != null && keyPressedCounter == 1) {
if (!inputTxt.getText().equalsIgnoreCase(welcomeText.get(jumpType))) {
inputTxt.setForeground(Color.black);
} else {
inputTxt.setForeground(new Color(204, 204, 204));
}
if (event.getKeyCode() == KeyEvent.VK_UP && previousButton.isEnabled()) {
previousButtonActionPerformed(null);
} else if (event.getKeyCode() == KeyEvent.VK_DOWN && nextButton.isEnabled()) {
nextButtonActionPerformed(null);
} else {
if (!possibilities.containsKey(jumpType)) {
possibilities.put(jumpType, new ArrayList<String>());
types.put(jumpType, new ArrayList<Type>());
} else {
possibilities.get(jumpType).clear();
types.get(jumpType).clear();
}
currentSelection.put(jumpType, 0);
String doubleString, input = inputTxt.getText().trim().toLowerCase();
lastInput.put(jumpType, input);
if (!input.equals("")) {
peptideShakerGUI.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
inputTxt.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
if (jumpType == JumpType.proteinAndPeptides) {
for (String proteinKey :
peptideShakerGUI
.getIdentificationFeaturesGenerator()
.getProcessedProteinKeys(null, peptideShakerGUI.getFilterPreferences())) {
if (!ProteinMatch.isDecoy(proteinKey)) {
if (proteinKey.toLowerCase().contains(input)) {
possibilities.get(jumpType).add(proteinKey);
types.get(jumpType).add(Type.PROTEIN);
} else {
try {
for (String accession : ProteinMatch.getAccessions(proteinKey)) {
if (sequenceFactory
.getHeader(accession)
.getSimpleProteinDescription()
.toLowerCase()
.contains(input)) {
possibilities.get(jumpType).add(proteinKey);
types.get(jumpType).add(Type.PROTEIN);
break;
}
}
} catch (Exception e) {
// cannot get description, ignore
}
}
}
}
// check if it's a valid peptide sequence
boolean validPeptideSequence;
try {
AminoAcid.getMatchingSequence(
input,
peptideShakerGUI
.getIdentificationParameters()
.getSequenceMatchingPreferences());
validPeptideSequence = true;
} catch (IllegalArgumentException e) {
// ignore, not a peptide sequence
validPeptideSequence = false;
}
if (validPeptideSequence) {
ArrayList<String> secondaryCandidates = new ArrayList<String>();
// pre-caching
PSParameter psParameter = new PSParameter();
identification.loadPeptideMatchParameters(psParameter, null, false);
String matchingInput =
AminoAcid.getMatchingSequence(
input,
peptideShakerGUI
.getIdentificationParameters()
.getSequenceMatchingPreferences());
for (String peptideKey : identification.getPeptideIdentification()) {
try {
psParameter =
(PSParameter)
identification.getPeptideMatchParameter(peptideKey, psParameter);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
return;
}
if (!psParameter.isHidden()) {
if (peptideKey.startsWith(matchingInput)) {
possibilities.get(jumpType).add(peptideKey);
types.get(jumpType).add(Type.PEPTIDE);
} else if (peptideKey.toLowerCase().contains(matchingInput)) {
secondaryCandidates.add(peptideKey);
}
}
}
PeptideMatchesIterator peptideMatchesIterator =
identification.getPeptideMatchesIterator(
secondaryCandidates,
null,
false,
null,
null); // @TODO: waiting handler?
while (peptideMatchesIterator.hasNext()) {
try {
PeptideMatch peptideMatch = peptideMatchesIterator.next();
String peptideKey = peptideMatch.getKey();
ArrayList<String> proteins =
peptideMatch.getTheoreticPeptide().getParentProteinsNoRemapping();
if (proteins != null) {
for (String protein : proteins) {
if (!ProteinMatch.isDecoy(protein)) {
possibilities.get(jumpType).add(peptideKey);
types.get(jumpType).add(Type.PEPTIDE);
break;
}
}
}
} catch (Exception e) {
peptideShakerGUI.catchException(e);
return;
}
}
}
} else {
for (String spectrumTitle : spectrumFactory.getSpectrumTitles(spectrumfile)) {
String spectrumKey = Spectrum.getSpectrumKey(spectrumfile, spectrumTitle);
if (spectrumKey.toLowerCase().contains(input)) {
possibilities.get(jumpType).add(spectrumKey);
types.get(jumpType).add(Type.SPECTRUM);
} else {
try {
Precursor precursor = spectrumFactory.getPrecursor(spectrumKey);
doubleString = precursor.getMz() + "";
if (doubleString.startsWith(input)) {
possibilities.get(jumpType).add(spectrumKey);
types.get(jumpType).add(Type.SPECTRUM);
} else {
doubleString = precursor.getRt() + "";
if (doubleString.startsWith(input)) {
possibilities.get(jumpType).add(spectrumKey);
types.get(jumpType).add(Type.SPECTRUM);
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
}
if (possibilities.get(jumpType).size() > 0) {
if (possibilities.get(jumpType).size() > 1) {
previousButton.setEnabled(true);
nextButton.setEnabled(true);
} else { // possibilities.size() == 1
previousButton.setEnabled(false);
nextButton.setEnabled(false);
}
updateSelectionInTab();
} else {
previousButton.setEnabled(false);
nextButton.setEnabled(false);
if (!input.equalsIgnoreCase(welcomeText.get(jumpType))) {
indexLabel.setText("(no matches)");
} else {
indexLabel.setText("");
}
}
peptideShakerGUI.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
inputTxt.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
} else {
indexLabel.setText("");
previousButton.setEnabled(false);
nextButton.setEnabled(false);
inputTxt.setText(welcomeText.get(jumpType));
inputTxt.selectAll();
}
}
lastLabel.put(jumpType, indexLabel.getText());
// gui updated, reset the counter
keyPressedCounter = 0;
} else {
// gui not updated, decrease the counter
keyPressedCounter--;
}
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
}
}.start();
} // GEN-LAST:event_inputTxtKeyReleased
/**
* Display the previous match in the list.
*
* @param evt the action event
*/
private void previousButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_previousButtonActionPerformed
if (currentSelection.get(jumpType) == 0) {
currentSelection.put(jumpType, possibilities.get(jumpType).size() - 1);
} else {
currentSelection.put(jumpType, currentSelection.get(jumpType) - 1);
}
updateSelectionInTab();
} // GEN-LAST:event_previousButtonActionPerformed
/**
* Display the next match in the list.
*
* @param evt the action event
*/
private void nextButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_nextButtonActionPerformed
if (currentSelection.get(jumpType) == possibilities.get(jumpType).size() - 1) {
currentSelection.put(jumpType, 0);
} else {
currentSelection.put(jumpType, currentSelection.get(jumpType) + 1);
}
updateSelectionInTab();
} // GEN-LAST:event_nextButtonActionPerformed
/**
* Select all text in the search field.
*
* @param evt the mouse event
*/
private void inputTxtMouseReleased(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_inputTxtMouseReleased
if (inputTxt.getText().equals(welcomeText.get(jumpType))) {
inputTxt.selectAll();
}
} // GEN-LAST:event_inputTxtMouseReleased
/**
* Change the icon to a hand icon.
*
* @param evt the mouse event
*/
private void previousButtonMouseEntered(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_previousButtonMouseEntered
if (previousButton.isEnabled()) {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}
} // GEN-LAST:event_previousButtonMouseEntered
/**
* Change the icon back to the default icon.
*
* @param evt the mouse event
*/
private void previousButtonMouseExited(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_previousButtonMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
} // GEN-LAST:event_previousButtonMouseExited
/**
* Change the icon back to the default icon.
*
* @param evt the mouse event
*/
private void nextButtonMouseExited(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_nextButtonMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
} // GEN-LAST:event_nextButtonMouseExited
/**
* Change the icon to a hand icon.
*
* @param evt the mouse event
*/
private void nextButtonMouseEntered(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_nextButtonMouseEntered
if (nextButton.isEnabled()) {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}
} // GEN-LAST:event_nextButtonMouseEntered
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JLabel findJLabel;
private javax.swing.JLabel indexLabel;
private javax.swing.JTextField inputTxt;
private javax.swing.JButton nextButton;
private javax.swing.JButton previousButton;
// End of variables declaration//GEN-END:variables
@Override
public void setEnabled(boolean enabled) {
inputTxt.setEnabled(enabled);
indexLabel.setEnabled(enabled);
if (possibilities.size() > 0 && enabled) {
previousButton.setEnabled(true);
nextButton.setEnabled(true);
} else {
previousButton.setEnabled(false);
nextButton.setEnabled(false);
}
}
/**
* Changes the type of jumpToPanel.
*
* @param jumpType the new type of jump to panel
*/
public void setType(JumpType jumpType) {
this.jumpType = jumpType;
if (lastInput.get(jumpType) != null && !lastInput.get(jumpType).equals("")) {
inputTxt.setText(lastInput.get(jumpType));
indexLabel.setText(lastLabel.get(jumpType));
} else {
inputTxt.setText(welcomeText.get(jumpType));
indexLabel.setText("");
}
}
/**
* Sets the spectrum file inspected.
*
* @param spectrumFile the name of the spectrum file inspected
*/
public void setSpectrumFile(String spectrumFile) {
this.spectrumfile = spectrumFile;
}
}
/**
* Fills the PSM specific map.
*
* @param inputMap The input map
* @param waitingHandler the handler displaying feedback to the user
* @param shotgunProtocol information about the protocol
* @param identificationParameters the identification parameters
* @throws java.sql.SQLException exception thrown whenever an error occurred while interacting
* with the back-end database
* @throws java.io.IOException exception thrown whenever an error occurred while reading an
* external file
* @throws java.lang.ClassNotFoundException exception thrown whenever an error occurred while
* deserializing an object
* @throws java.lang.InterruptedException exception thrown whenever a threading error occurred
* @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException exception thrown whenever an error
* occurred while reading an mzML file
*/
public void selectBestHitAndFillPsmMap(
InputMap inputMap,
WaitingHandler waitingHandler,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters)
throws SQLException, IOException, ClassNotFoundException, InterruptedException,
MzMLUnmarshallerException {
waitingHandler.setSecondaryProgressCounterIndeterminate(false);
waitingHandler.setMaxSecondaryProgressCounter(identification.getSpectrumIdentificationSize());
PeptideSpectrumAnnotator spectrumAnnotator = new PeptideSpectrumAnnotator();
boolean multiSE = inputMap.isMultipleAlgorithms();
SequenceMatchingPreferences sequenceMatchingPreferences =
identificationParameters.getSequenceMatchingPreferences();
AnnotationSettings annotationPreferences = identificationParameters.getAnnotationPreferences();
PeptideAssumptionFilter idFilter = identificationParameters.getPeptideAssumptionFilter();
// Keep a map of the spectrum keys grouped by peptide
HashMap<String, ArrayList<String>> orderedPsmMap = null;
if (MemoryConsumptionStatus.memoryUsed() < 0.8) {
orderedPsmMap =
new HashMap<String, ArrayList<String>>(
identification.getSpectrumIdentificationMap().size());
}
PSParameter psParameter = new PSParameter();
for (String spectrumFileName : identification.getSpectrumFiles()) {
HashMap<String, ArrayList<String>> keysMap = null;
if (orderedPsmMap != null) {
keysMap = new HashMap<String, ArrayList<String>>();
}
PsmIterator psmIterator =
identification.getPsmIterator(spectrumFileName, null, true, waitingHandler);
while (psmIterator.hasNext()) {
SpectrumMatch advocateMatch = psmIterator.next();
String spectrumKey = advocateMatch.getKey();
// map of the peptide first hits for this spectrum: score -> max protein count -> max search
// engine votes -> amino acids annotated -> min mass deviation -> peptide sequence
HashMap<
Double,
HashMap<
Integer,
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>>
peptideAssumptions =
new HashMap<
Double,
HashMap<
Integer,
HashMap<
Integer,
HashMap<
Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>>();
// map of the tag first hits: score -> assumptions
HashMap<Double, ArrayList<TagAssumption>> tagAssumptions =
new HashMap<Double, ArrayList<TagAssumption>>();
ArrayList<String> identifications = new ArrayList<String>();
HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>> assumptions =
identification.getAssumptions(spectrumKey);
for (int searchEngine1 : assumptions.keySet()) {
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> advocate1Map =
assumptions.get(searchEngine1);
double bestEvalue = Collections.min(advocate1Map.keySet());
for (SpectrumIdentificationAssumption assumption1 : advocate1Map.get(bestEvalue)) {
if (assumption1 instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption1 = (PeptideAssumption) assumption1;
String id = peptideAssumption1.getPeptide().getKey();
if (!identifications.contains(id)) {
psParameter = (PSParameter) peptideAssumption1.getUrParam(psParameter);
double p;
if (multiSE && sequenceFactory.concatenatedTargetDecoy()) {
p = psParameter.getSearchEngineProbability();
} else {
p = peptideAssumption1.getScore();
}
int nSE = 1;
int proteinMax = 1;
for (String protein :
peptideAssumption1
.getPeptide()
.getParentProteins(sequenceMatchingPreferences)) {
Integer tempCount = proteinCount.get(protein);
if (tempCount != null && tempCount > proteinMax) {
proteinMax = tempCount;
}
}
for (int searchEngine2 : assumptions.keySet()) {
if (searchEngine1 != searchEngine2) {
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> advocate2Map =
assumptions.get(searchEngine2);
boolean found = false;
ArrayList<Double> eValues2 = new ArrayList<Double>(advocate2Map.keySet());
Collections.sort(eValues2);
for (double eValue2 : eValues2) {
for (SpectrumIdentificationAssumption assumption2 :
advocate2Map.get(eValue2)) {
if (assumption2 instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption2 = (PeptideAssumption) assumption2;
if (peptideAssumption1
.getPeptide()
.isSameSequenceAndModificationStatus(
peptideAssumption2.getPeptide(), sequenceMatchingPreferences)) {
PSParameter psParameter2 =
(PSParameter) peptideAssumption2.getUrParam(psParameter);
p = p * psParameter2.getSearchEngineProbability();
nSE++;
found = true;
break;
}
}
}
if (found) {
break;
}
}
}
}
identifications.add(id);
HashMap<
Integer,
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>
pMap = peptideAssumptions.get(p);
if (pMap == null) {
pMap =
new HashMap<
Integer,
HashMap<
Integer,
HashMap<
Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>(
advocate1Map.size());
peptideAssumptions.put(p, pMap);
}
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>
proteinMaxMap = pMap.get(proteinMax);
if (proteinMaxMap == null) {
proteinMaxMap =
new HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>(1);
pMap.put(proteinMax, proteinMaxMap);
}
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>> nSeMap =
proteinMaxMap.get(nSE);
if (nSeMap == null) {
nSeMap =
new HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>(1);
proteinMaxMap.put(nSE, nSeMap);
HashMap<Double, HashMap<String, PeptideAssumption>> coverageMap =
new HashMap<Double, HashMap<String, PeptideAssumption>>(1);
nSeMap.put(-1, coverageMap);
HashMap<String, PeptideAssumption> assumptionMap =
new HashMap<String, PeptideAssumption>(1);
coverageMap.put(-1.0, assumptionMap);
assumptionMap.put(
peptideAssumption1.getPeptide().getSequenceWithLowerCasePtms(),
peptideAssumption1);
} else {
MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
HashMap<Double, HashMap<String, PeptideAssumption>> coverageMap = nSeMap.get(-1);
if (coverageMap != null) {
HashMap<String, PeptideAssumption> assumptionMap = coverageMap.get(-1.0);
for (PeptideAssumption tempAssumption :
assumptionMap.values()) { // There should be only one
Peptide peptide = tempAssumption.getPeptide();
SpecificAnnotationSettings specificAnnotationPreferences =
annotationPreferences.getSpecificAnnotationPreferences(
spectrum.getSpectrumKey(),
tempAssumption,
identificationParameters.getSequenceMatchingPreferences(),
identificationParameters
.getPtmScoringPreferences()
.getSequenceMatchingPreferences());
HashMap<Integer, ArrayList<IonMatch>> coveredAminoAcids =
spectrumAnnotator.getCoveredAminoAcids(
annotationPreferences,
specificAnnotationPreferences,
(MSnSpectrum) spectrum,
peptide);
int nIons = coveredAminoAcids.size();
nSeMap.put(nIons, coverageMap);
}
nSeMap.remove(-1);
}
Peptide peptide = peptideAssumption1.getPeptide();
SpecificAnnotationSettings specificAnnotationPreferences =
annotationPreferences.getSpecificAnnotationPreferences(
spectrum.getSpectrumKey(),
peptideAssumption1,
identificationParameters.getSequenceMatchingPreferences(),
identificationParameters
.getPtmScoringPreferences()
.getSequenceMatchingPreferences());
HashMap<Integer, ArrayList<IonMatch>> coveredAminoAcids =
spectrumAnnotator.getCoveredAminoAcids(
annotationPreferences,
specificAnnotationPreferences,
(MSnSpectrum) spectrum,
peptide);
int nIons = coveredAminoAcids.size();
coverageMap = nSeMap.get(nIons);
if (coverageMap == null) {
coverageMap = new HashMap<Double, HashMap<String, PeptideAssumption>>(1);
HashMap<String, PeptideAssumption> assumptionMap =
new HashMap<String, PeptideAssumption>(1);
assumptionMap.put(
peptideAssumption1.getPeptide().getSequenceWithLowerCasePtms(),
peptideAssumption1);
coverageMap.put(-1.0, assumptionMap);
nSeMap.put(nIons, coverageMap);
} else {
HashMap<String, PeptideAssumption> assumptionMap = coverageMap.get(-1.0);
if (assumptionMap != null) {
for (PeptideAssumption tempAssumption :
assumptionMap.values()) { // There should be only one
double massError =
Math.abs(
tempAssumption.getDeltaMass(
spectrum.getPrecursor().getMz(),
shotgunProtocol.isMs1ResolutionPpm()));
coverageMap.put(massError, assumptionMap);
}
coverageMap.remove(-1.0);
}
double massError =
Math.abs(
peptideAssumption1.getDeltaMass(
spectrum.getPrecursor().getMz(),
shotgunProtocol.isMs1ResolutionPpm()));
assumptionMap = coverageMap.get(massError);
if (assumptionMap == null) {
assumptionMap = new HashMap<String, PeptideAssumption>(1);
coverageMap.put(massError, assumptionMap);
}
assumptionMap.put(
peptideAssumption1.getPeptide().getSequenceWithLowerCasePtms(),
peptideAssumption1);
}
}
}
} else if (assumption1 instanceof TagAssumption) {
TagAssumption tagAssumption = (TagAssumption) assumption1;
ArrayList<TagAssumption> assumptionList = tagAssumptions.get(bestEvalue);
if (assumptionList == null) {
assumptionList = new ArrayList<TagAssumption>();
tagAssumptions.put(bestEvalue, assumptionList);
}
assumptionList.add(tagAssumption);
}
}
}
SpectrumMatch spectrumMatch = new SpectrumMatch(spectrumKey);
if (!peptideAssumptions.isEmpty()) {
PeptideAssumption bestPeptideAssumption = null;
ArrayList<Double> ps = new ArrayList<Double>(peptideAssumptions.keySet());
Collections.sort(ps);
double retainedP = 0;
for (double p : ps) {
retainedP = p;
HashMap<
Integer,
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>
pMap = peptideAssumptions.get(p);
ArrayList<Integer> proteinMaxs = new ArrayList<Integer>(pMap.keySet());
Collections.sort(proteinMaxs, Collections.reverseOrder());
for (int proteinMax : proteinMaxs) {
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>
proteinMaxMap = pMap.get(proteinMax);
ArrayList<Integer> nSEs = new ArrayList<Integer>(proteinMaxMap.keySet());
Collections.sort(nSEs, Collections.reverseOrder());
for (int nSE : nSEs) {
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>> nSeMap =
proteinMaxMap.get(nSE);
ArrayList<Integer> coverages = new ArrayList<Integer>(nSeMap.keySet());
Collections.sort(coverages, Collections.reverseOrder());
for (Integer coverage : coverages) {
HashMap<Double, HashMap<String, PeptideAssumption>> coverageMap =
nSeMap.get(coverage);
ArrayList<Double> minErrors = new ArrayList<Double>(coverageMap.keySet());
Collections.sort(minErrors);
for (double minError : minErrors) {
HashMap<String, PeptideAssumption> bestPeptideAssumptions =
coverageMap.get(minError);
ArrayList<String> sequences =
new ArrayList<String>(bestPeptideAssumptions.keySet());
Collections.sort(sequences);
for (String sequence : sequences) {
PeptideAssumption peptideAssumption = bestPeptideAssumptions.get(sequence);
if (idFilter.validateProteins(
peptideAssumption.getPeptide(), sequenceMatchingPreferences)) {
bestPeptideAssumption = peptideAssumption;
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
if (multiSE) {
// try to find the most likely modification localization based on the search engine
// results
HashMap<PeptideAssumption, ArrayList<Double>> assumptionPEPs =
new HashMap<PeptideAssumption, ArrayList<Double>>();
String bestAssumptionKey =
bestPeptideAssumption.getPeptide().getMatchingKey(sequenceMatchingPreferences);
for (int searchEngine : assumptions.keySet()) {
boolean found = false;
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> advocateMap =
assumptions.get(searchEngine);
ArrayList<Double> eValues = new ArrayList<Double>(advocateMap.keySet());
Collections.sort(eValues);
for (double eValue : eValues) {
for (SpectrumIdentificationAssumption assumption : advocateMap.get(eValue)) {
if (assumption instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;
if (peptideAssumption
.getPeptide()
.getMatchingKey(sequenceMatchingPreferences)
.equals(bestAssumptionKey)) {
found = true;
boolean found2 = false;
for (PeptideAssumption assumption1 : assumptionPEPs.keySet()) {
if (assumption1
.getPeptide()
.sameModificationsAs(peptideAssumption.getPeptide())) {
found2 = true;
psParameter = (PSParameter) assumption.getUrParam(psParameter);
ArrayList<Double> peps = assumptionPEPs.get(assumption1);
peps.add(psParameter.getSearchEngineProbability());
break;
}
}
if (!found2) {
ArrayList<Double> peps = new ArrayList<Double>(1);
assumptionPEPs.put(peptideAssumption, peps);
psParameter = (PSParameter) assumption.getUrParam(psParameter);
peps.add(psParameter.getSearchEngineProbability());
}
}
}
}
if (found) {
break;
}
}
}
Double bestSeP = null;
int nSe = -1;
for (PeptideAssumption peptideAssumption : assumptionPEPs.keySet()) {
ArrayList<Double> peps = assumptionPEPs.get(peptideAssumption);
Double sep = Collections.min(peps);
if (bestSeP == null || bestSeP > sep) {
bestSeP = sep;
nSe = peps.size();
bestPeptideAssumption = peptideAssumption;
} else if (peps.size() > nSe) {
if (sep != null && (Math.abs(sep - bestSeP) <= 1e-10)) {
nSe = peps.size();
bestPeptideAssumption = peptideAssumption;
}
}
}
}
// create a PeptideShaker match based on the best search engine match
Peptide sePeptide = bestPeptideAssumption.getPeptide();
ArrayList<String> psProteins =
new ArrayList<String>(sePeptide.getParentProteins(sequenceMatchingPreferences));
ArrayList<ModificationMatch> psModificationMatches = null;
if (sePeptide.isModified()) {
psModificationMatches =
new ArrayList<ModificationMatch>(sePeptide.getNModifications());
for (ModificationMatch seModMatch : sePeptide.getModificationMatches()) {
psModificationMatches.add(
new ModificationMatch(
seModMatch.getTheoreticPtm(),
seModMatch.isVariable(),
seModMatch.getModificationSite()));
}
}
Peptide psPeptide = new Peptide(sePeptide.getSequence(), psModificationMatches);
psPeptide.setParentProteins(psProteins);
PeptideAssumption psAssumption =
new PeptideAssumption(
psPeptide,
1,
Advocate.peptideShaker.getIndex(),
bestPeptideAssumption.getIdentificationCharge(),
retainedP);
spectrumMatch.setBestPeptideAssumption(psAssumption);
if (orderedPsmMap != null) {
String peptideKey = psPeptide.getMatchingKey(sequenceMatchingPreferences);
ArrayList<String> spectrumKeys = keysMap.get(peptideKey);
if (spectrumKeys == null) {
spectrumKeys = new ArrayList<String>();
keysMap.put(peptideKey, spectrumKeys);
}
spectrumKeys.add(spectrumKey);
}
psParameter = new PSParameter();
psParameter.setSpectrumProbabilityScore(retainedP);
PSParameter matchParameter =
(PSParameter) bestPeptideAssumption.getUrParam(psParameter);
psParameter.setSearchEngineProbability(matchParameter.getSearchEngineProbability());
psParameter.setAlgorithmDeltaPEP(matchParameter.getAlgorithmDeltaPEP());
psParameter.setDeltaPEP(matchParameter.getDeltaPEP());
matchesValidator
.getPsmMap()
.addPoint(
psParameter.getPsmProbabilityScore(),
spectrumMatch,
sequenceMatchingPreferences);
psParameter.setSpecificMapKey(
spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value + "");
identification.addSpectrumMatchParameter(spectrumKey, psParameter);
identification.updateSpectrumMatch(spectrumMatch);
}
}
if (!tagAssumptions.isEmpty()) {
ArrayList<Double> evalues = new ArrayList<Double>(tagAssumptions.keySet());
Double bestEvalue = Collections.min(evalues);
TagAssumption bestAssumption = tagAssumptions.get(bestEvalue).get(0);
spectrumMatch.setBestTagAssumption(bestAssumption);
identification.updateSpectrumMatch(spectrumMatch);
if (spectrumMatch.getBestPeptideAssumption() == null) {
psParameter = new PSParameter();
if (!multiSE) {
psParameter.setSpectrumProbabilityScore(bestEvalue);
}
PSParameter matchParameter = (PSParameter) bestAssumption.getUrParam(psParameter);
psParameter.setSearchEngineProbability(matchParameter.getSearchEngineProbability());
psParameter.setAlgorithmDeltaPEP(matchParameter.getAlgorithmDeltaPEP());
psParameter.setDeltaPEP(matchParameter.getDeltaPEP());
psParameter.setSpecificMapKey(
spectrumMatch.getBestTagAssumption().getIdentificationCharge().value + "");
identification.addSpectrumMatchParameter(spectrumKey, psParameter);
}
}
waitingHandler.increaseSecondaryProgressCounter();
if (waitingHandler.isRunCanceled()) {
return;
}
}
if (orderedPsmMap != null) {
ArrayList<String> orderedKeys =
new ArrayList<String>(
identification.getSpectrumIdentification(spectrumFileName).size());
for (ArrayList<String> keys : keysMap.values()) {
orderedKeys.addAll(keys);
}
orderedPsmMap.put(spectrumFileName, orderedKeys);
if (MemoryConsumptionStatus.memoryUsed() > 0.9) {
orderedPsmMap = null;
}
}
}
if (orderedPsmMap != null) {
metrics.setOrderedSpectrumKeys(orderedPsmMap);
}
// the protein count map is no longer needed
proteinCount.clear();
waitingHandler.setSecondaryProgressCounterIndeterminate(true);
}
/**
* Selects a first hit in a list of equally scoring peptide matches. The selection is made based
* on: 1 - The occurrence of the protein detection as given in the proteinCount map 2 - The
* sequence coverage by fragment ions 3 - The precursor mass error.
*
* <p>If no best hit is found, the first one sorted alphabetically is retained.
*
* @param spectrumKey the key of the spectrum
* @param firstHits list of equally scoring peptide matches
* @param proteinCount map of the number of peptides for every protein
* @param sequenceMatchingPreferences the sequence matching preferences
* @param shotgunProtocol the shotgun protocol
* @param identificationParameters the identification parameters
* @param spectrumAnnotator the spectrum annotator to use
* @return a first hit from the list of equally scoring peptide matches
* @throws IOException exception thrown whenever an IO exception occurred while remapping the
* proteins or getting the spectrum
* @throws InterruptedException exception thrown whenever an interrupted exception occurred while
* remapping the proteins or getting the spectrum
* @throws SQLException exception thrown whenever an SQL exception occurred while interacting with
* the protein tree
* @throws ClassNotFoundException exception thrown whenever an exception occurred while
* deserializing an object
* @throws MzMLUnmarshallerException exception thrown whenever an exception occurred while reading
* an mzML file
*/
public static PeptideAssumption getBestHit(
String spectrumKey,
ArrayList<PeptideAssumption> firstHits,
HashMap<String, Integer> proteinCount,
SequenceMatchingPreferences sequenceMatchingPreferences,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
PeptideSpectrumAnnotator spectrumAnnotator)
throws IOException, InterruptedException, SQLException, ClassNotFoundException,
MzMLUnmarshallerException {
if (firstHits.size() == 1) {
return firstHits.get(0);
}
Integer maxProteins = 0;
ArrayList<PeptideAssumption> bestPeptideAssumptions =
new ArrayList<PeptideAssumption>(firstHits.size());
for (PeptideAssumption peptideAssumption : firstHits) {
for (String accession :
peptideAssumption.getPeptide().getParentProteins(sequenceMatchingPreferences)) {
Integer count = proteinCount.get(accession);
if (count != null) {
if (count > maxProteins) {
maxProteins = count;
bestPeptideAssumptions.clear();
bestPeptideAssumptions.add(peptideAssumption);
} else if (count.equals(maxProteins)) {
bestPeptideAssumptions.add(peptideAssumption);
}
}
}
}
if (bestPeptideAssumptions.size() == 1) {
return bestPeptideAssumptions.get(0);
} else if (!bestPeptideAssumptions.isEmpty()) {
firstHits = bestPeptideAssumptions;
bestPeptideAssumptions = new ArrayList<PeptideAssumption>(firstHits.size());
}
MSnSpectrum spectrum = (MSnSpectrum) SpectrumFactory.getInstance().getSpectrum(spectrumKey);
int maxCoveredAminoAcids = 0;
AnnotationSettings annotationPreferences = identificationParameters.getAnnotationPreferences();
for (PeptideAssumption peptideAssumption : firstHits) {
Peptide peptide = peptideAssumption.getPeptide();
SpecificAnnotationSettings specificAnnotationPreferences =
annotationPreferences.getSpecificAnnotationPreferences(
spectrum.getSpectrumKey(),
peptideAssumption,
identificationParameters.getSequenceMatchingPreferences(),
identificationParameters.getPtmScoringPreferences().getSequenceMatchingPreferences());
HashMap<Integer, ArrayList<IonMatch>> coveredAminoAcids =
spectrumAnnotator.getCoveredAminoAcids(
annotationPreferences,
specificAnnotationPreferences,
(MSnSpectrum) spectrum,
peptide);
int nAas = coveredAminoAcids.size();
if (nAas > maxCoveredAminoAcids) {
maxCoveredAminoAcids = nAas;
bestPeptideAssumptions.clear();
bestPeptideAssumptions.add(peptideAssumption);
} else if (nAas == maxCoveredAminoAcids) {
bestPeptideAssumptions.add(peptideAssumption);
}
}
if (bestPeptideAssumptions.size() == 1) {
return bestPeptideAssumptions.get(0);
} else if (!bestPeptideAssumptions.isEmpty()) {
firstHits = bestPeptideAssumptions;
bestPeptideAssumptions = new ArrayList<PeptideAssumption>(firstHits.size());
}
double minMassError = identificationParameters.getPeptideAssumptionFilter().getMaxMzDeviation();
if (minMassError == -1.0) {
minMassError = identificationParameters.getSearchParameters().getPrecursorAccuracy();
}
for (PeptideAssumption peptideAssumption : firstHits) {
double massError =
Math.abs(
peptideAssumption.getDeltaMass(
spectrum.getPrecursor().getMz(), shotgunProtocol.isMs1ResolutionPpm()));
if (massError < minMassError) {
minMassError = massError;
bestPeptideAssumptions.clear();
bestPeptideAssumptions.add(peptideAssumption);
} else if (massError == minMassError) {
bestPeptideAssumptions.add(peptideAssumption);
}
}
if (bestPeptideAssumptions.size() == 1) {
return bestPeptideAssumptions.get(0);
} else if (bestPeptideAssumptions.isEmpty()) {
bestPeptideAssumptions = firstHits;
}
HashMap<String, PeptideAssumption> sequenceToPeptideAssumptionsMap =
new HashMap<String, PeptideAssumption>(bestPeptideAssumptions.size());
for (PeptideAssumption peptideAssumption : bestPeptideAssumptions) {
sequenceToPeptideAssumptionsMap.put(
peptideAssumption.getPeptide().getSequence(), peptideAssumption);
}
ArrayList<String> sequences = new ArrayList<String>(sequenceToPeptideAssumptionsMap.keySet());
Collections.sort(sequences);
return sequenceToPeptideAssumptionsMap.get(sequences.get(0));
}
/**
* This class contains the method for PSM best hit selection.
*
* @author Marc Vaudel
*/
public class BestMatchSelection {
/** The sequence factory. */
private SequenceFactory sequenceFactory = SequenceFactory.getInstance();
/** The spectrum factory. */
private SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
/**
* Map indicating how often a protein was found in a search engine first hit whenever this protein
* was found more than one time.
*/
private HashMap<String, Integer> proteinCount = new HashMap<String, Integer>();
/** The identification object. */
private Identification identification;
/** The validator which will take care of the matches validation. */
private MatchesValidator matchesValidator;
/** Metrics to be picked when loading the identification. */
private Metrics metrics = new Metrics();
/**
* Constructor.
*
* @param identification the identification object where to get the matches from
* @param proteinCount a map of proteins found multiple times
* @param matchesValidator the matches validator
* @param metrics the object where to store dataset metrics
*/
public BestMatchSelection(
Identification identification,
HashMap<String, Integer> proteinCount,
MatchesValidator matchesValidator,
Metrics metrics) {
this.identification = identification;
this.proteinCount = proteinCount;
this.matchesValidator = matchesValidator;
this.metrics = metrics;
}
/**
* Fills the PSM specific map.
*
* @param inputMap The input map
* @param waitingHandler the handler displaying feedback to the user
* @param shotgunProtocol information about the protocol
* @param identificationParameters the identification parameters
* @throws java.sql.SQLException exception thrown whenever an error occurred while interacting
* with the back-end database
* @throws java.io.IOException exception thrown whenever an error occurred while reading an
* external file
* @throws java.lang.ClassNotFoundException exception thrown whenever an error occurred while
* deserializing an object
* @throws java.lang.InterruptedException exception thrown whenever a threading error occurred
* @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException exception thrown whenever an error
* occurred while reading an mzML file
*/
public void selectBestHitAndFillPsmMap(
InputMap inputMap,
WaitingHandler waitingHandler,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters)
throws SQLException, IOException, ClassNotFoundException, InterruptedException,
MzMLUnmarshallerException {
waitingHandler.setSecondaryProgressCounterIndeterminate(false);
waitingHandler.setMaxSecondaryProgressCounter(identification.getSpectrumIdentificationSize());
PeptideSpectrumAnnotator spectrumAnnotator = new PeptideSpectrumAnnotator();
boolean multiSE = inputMap.isMultipleAlgorithms();
SequenceMatchingPreferences sequenceMatchingPreferences =
identificationParameters.getSequenceMatchingPreferences();
AnnotationSettings annotationPreferences = identificationParameters.getAnnotationPreferences();
PeptideAssumptionFilter idFilter = identificationParameters.getPeptideAssumptionFilter();
// Keep a map of the spectrum keys grouped by peptide
HashMap<String, ArrayList<String>> orderedPsmMap = null;
if (MemoryConsumptionStatus.memoryUsed() < 0.8) {
orderedPsmMap =
new HashMap<String, ArrayList<String>>(
identification.getSpectrumIdentificationMap().size());
}
PSParameter psParameter = new PSParameter();
for (String spectrumFileName : identification.getSpectrumFiles()) {
HashMap<String, ArrayList<String>> keysMap = null;
if (orderedPsmMap != null) {
keysMap = new HashMap<String, ArrayList<String>>();
}
PsmIterator psmIterator =
identification.getPsmIterator(spectrumFileName, null, true, waitingHandler);
while (psmIterator.hasNext()) {
SpectrumMatch advocateMatch = psmIterator.next();
String spectrumKey = advocateMatch.getKey();
// map of the peptide first hits for this spectrum: score -> max protein count -> max search
// engine votes -> amino acids annotated -> min mass deviation -> peptide sequence
HashMap<
Double,
HashMap<
Integer,
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>>
peptideAssumptions =
new HashMap<
Double,
HashMap<
Integer,
HashMap<
Integer,
HashMap<
Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>>();
// map of the tag first hits: score -> assumptions
HashMap<Double, ArrayList<TagAssumption>> tagAssumptions =
new HashMap<Double, ArrayList<TagAssumption>>();
ArrayList<String> identifications = new ArrayList<String>();
HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>> assumptions =
identification.getAssumptions(spectrumKey);
for (int searchEngine1 : assumptions.keySet()) {
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> advocate1Map =
assumptions.get(searchEngine1);
double bestEvalue = Collections.min(advocate1Map.keySet());
for (SpectrumIdentificationAssumption assumption1 : advocate1Map.get(bestEvalue)) {
if (assumption1 instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption1 = (PeptideAssumption) assumption1;
String id = peptideAssumption1.getPeptide().getKey();
if (!identifications.contains(id)) {
psParameter = (PSParameter) peptideAssumption1.getUrParam(psParameter);
double p;
if (multiSE && sequenceFactory.concatenatedTargetDecoy()) {
p = psParameter.getSearchEngineProbability();
} else {
p = peptideAssumption1.getScore();
}
int nSE = 1;
int proteinMax = 1;
for (String protein :
peptideAssumption1
.getPeptide()
.getParentProteins(sequenceMatchingPreferences)) {
Integer tempCount = proteinCount.get(protein);
if (tempCount != null && tempCount > proteinMax) {
proteinMax = tempCount;
}
}
for (int searchEngine2 : assumptions.keySet()) {
if (searchEngine1 != searchEngine2) {
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> advocate2Map =
assumptions.get(searchEngine2);
boolean found = false;
ArrayList<Double> eValues2 = new ArrayList<Double>(advocate2Map.keySet());
Collections.sort(eValues2);
for (double eValue2 : eValues2) {
for (SpectrumIdentificationAssumption assumption2 :
advocate2Map.get(eValue2)) {
if (assumption2 instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption2 = (PeptideAssumption) assumption2;
if (peptideAssumption1
.getPeptide()
.isSameSequenceAndModificationStatus(
peptideAssumption2.getPeptide(), sequenceMatchingPreferences)) {
PSParameter psParameter2 =
(PSParameter) peptideAssumption2.getUrParam(psParameter);
p = p * psParameter2.getSearchEngineProbability();
nSE++;
found = true;
break;
}
}
}
if (found) {
break;
}
}
}
}
identifications.add(id);
HashMap<
Integer,
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>
pMap = peptideAssumptions.get(p);
if (pMap == null) {
pMap =
new HashMap<
Integer,
HashMap<
Integer,
HashMap<
Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>(
advocate1Map.size());
peptideAssumptions.put(p, pMap);
}
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>
proteinMaxMap = pMap.get(proteinMax);
if (proteinMaxMap == null) {
proteinMaxMap =
new HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>(1);
pMap.put(proteinMax, proteinMaxMap);
}
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>> nSeMap =
proteinMaxMap.get(nSE);
if (nSeMap == null) {
nSeMap =
new HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>(1);
proteinMaxMap.put(nSE, nSeMap);
HashMap<Double, HashMap<String, PeptideAssumption>> coverageMap =
new HashMap<Double, HashMap<String, PeptideAssumption>>(1);
nSeMap.put(-1, coverageMap);
HashMap<String, PeptideAssumption> assumptionMap =
new HashMap<String, PeptideAssumption>(1);
coverageMap.put(-1.0, assumptionMap);
assumptionMap.put(
peptideAssumption1.getPeptide().getSequenceWithLowerCasePtms(),
peptideAssumption1);
} else {
MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
HashMap<Double, HashMap<String, PeptideAssumption>> coverageMap = nSeMap.get(-1);
if (coverageMap != null) {
HashMap<String, PeptideAssumption> assumptionMap = coverageMap.get(-1.0);
for (PeptideAssumption tempAssumption :
assumptionMap.values()) { // There should be only one
Peptide peptide = tempAssumption.getPeptide();
SpecificAnnotationSettings specificAnnotationPreferences =
annotationPreferences.getSpecificAnnotationPreferences(
spectrum.getSpectrumKey(),
tempAssumption,
identificationParameters.getSequenceMatchingPreferences(),
identificationParameters
.getPtmScoringPreferences()
.getSequenceMatchingPreferences());
HashMap<Integer, ArrayList<IonMatch>> coveredAminoAcids =
spectrumAnnotator.getCoveredAminoAcids(
annotationPreferences,
specificAnnotationPreferences,
(MSnSpectrum) spectrum,
peptide);
int nIons = coveredAminoAcids.size();
nSeMap.put(nIons, coverageMap);
}
nSeMap.remove(-1);
}
Peptide peptide = peptideAssumption1.getPeptide();
SpecificAnnotationSettings specificAnnotationPreferences =
annotationPreferences.getSpecificAnnotationPreferences(
spectrum.getSpectrumKey(),
peptideAssumption1,
identificationParameters.getSequenceMatchingPreferences(),
identificationParameters
.getPtmScoringPreferences()
.getSequenceMatchingPreferences());
HashMap<Integer, ArrayList<IonMatch>> coveredAminoAcids =
spectrumAnnotator.getCoveredAminoAcids(
annotationPreferences,
specificAnnotationPreferences,
(MSnSpectrum) spectrum,
peptide);
int nIons = coveredAminoAcids.size();
coverageMap = nSeMap.get(nIons);
if (coverageMap == null) {
coverageMap = new HashMap<Double, HashMap<String, PeptideAssumption>>(1);
HashMap<String, PeptideAssumption> assumptionMap =
new HashMap<String, PeptideAssumption>(1);
assumptionMap.put(
peptideAssumption1.getPeptide().getSequenceWithLowerCasePtms(),
peptideAssumption1);
coverageMap.put(-1.0, assumptionMap);
nSeMap.put(nIons, coverageMap);
} else {
HashMap<String, PeptideAssumption> assumptionMap = coverageMap.get(-1.0);
if (assumptionMap != null) {
for (PeptideAssumption tempAssumption :
assumptionMap.values()) { // There should be only one
double massError =
Math.abs(
tempAssumption.getDeltaMass(
spectrum.getPrecursor().getMz(),
shotgunProtocol.isMs1ResolutionPpm()));
coverageMap.put(massError, assumptionMap);
}
coverageMap.remove(-1.0);
}
double massError =
Math.abs(
peptideAssumption1.getDeltaMass(
spectrum.getPrecursor().getMz(),
shotgunProtocol.isMs1ResolutionPpm()));
assumptionMap = coverageMap.get(massError);
if (assumptionMap == null) {
assumptionMap = new HashMap<String, PeptideAssumption>(1);
coverageMap.put(massError, assumptionMap);
}
assumptionMap.put(
peptideAssumption1.getPeptide().getSequenceWithLowerCasePtms(),
peptideAssumption1);
}
}
}
} else if (assumption1 instanceof TagAssumption) {
TagAssumption tagAssumption = (TagAssumption) assumption1;
ArrayList<TagAssumption> assumptionList = tagAssumptions.get(bestEvalue);
if (assumptionList == null) {
assumptionList = new ArrayList<TagAssumption>();
tagAssumptions.put(bestEvalue, assumptionList);
}
assumptionList.add(tagAssumption);
}
}
}
SpectrumMatch spectrumMatch = new SpectrumMatch(spectrumKey);
if (!peptideAssumptions.isEmpty()) {
PeptideAssumption bestPeptideAssumption = null;
ArrayList<Double> ps = new ArrayList<Double>(peptideAssumptions.keySet());
Collections.sort(ps);
double retainedP = 0;
for (double p : ps) {
retainedP = p;
HashMap<
Integer,
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>>
pMap = peptideAssumptions.get(p);
ArrayList<Integer> proteinMaxs = new ArrayList<Integer>(pMap.keySet());
Collections.sort(proteinMaxs, Collections.reverseOrder());
for (int proteinMax : proteinMaxs) {
HashMap<
Integer,
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>>>
proteinMaxMap = pMap.get(proteinMax);
ArrayList<Integer> nSEs = new ArrayList<Integer>(proteinMaxMap.keySet());
Collections.sort(nSEs, Collections.reverseOrder());
for (int nSE : nSEs) {
HashMap<Integer, HashMap<Double, HashMap<String, PeptideAssumption>>> nSeMap =
proteinMaxMap.get(nSE);
ArrayList<Integer> coverages = new ArrayList<Integer>(nSeMap.keySet());
Collections.sort(coverages, Collections.reverseOrder());
for (Integer coverage : coverages) {
HashMap<Double, HashMap<String, PeptideAssumption>> coverageMap =
nSeMap.get(coverage);
ArrayList<Double> minErrors = new ArrayList<Double>(coverageMap.keySet());
Collections.sort(minErrors);
for (double minError : minErrors) {
HashMap<String, PeptideAssumption> bestPeptideAssumptions =
coverageMap.get(minError);
ArrayList<String> sequences =
new ArrayList<String>(bestPeptideAssumptions.keySet());
Collections.sort(sequences);
for (String sequence : sequences) {
PeptideAssumption peptideAssumption = bestPeptideAssumptions.get(sequence);
if (idFilter.validateProteins(
peptideAssumption.getPeptide(), sequenceMatchingPreferences)) {
bestPeptideAssumption = peptideAssumption;
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
break;
}
}
if (bestPeptideAssumption != null) {
if (multiSE) {
// try to find the most likely modification localization based on the search engine
// results
HashMap<PeptideAssumption, ArrayList<Double>> assumptionPEPs =
new HashMap<PeptideAssumption, ArrayList<Double>>();
String bestAssumptionKey =
bestPeptideAssumption.getPeptide().getMatchingKey(sequenceMatchingPreferences);
for (int searchEngine : assumptions.keySet()) {
boolean found = false;
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> advocateMap =
assumptions.get(searchEngine);
ArrayList<Double> eValues = new ArrayList<Double>(advocateMap.keySet());
Collections.sort(eValues);
for (double eValue : eValues) {
for (SpectrumIdentificationAssumption assumption : advocateMap.get(eValue)) {
if (assumption instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;
if (peptideAssumption
.getPeptide()
.getMatchingKey(sequenceMatchingPreferences)
.equals(bestAssumptionKey)) {
found = true;
boolean found2 = false;
for (PeptideAssumption assumption1 : assumptionPEPs.keySet()) {
if (assumption1
.getPeptide()
.sameModificationsAs(peptideAssumption.getPeptide())) {
found2 = true;
psParameter = (PSParameter) assumption.getUrParam(psParameter);
ArrayList<Double> peps = assumptionPEPs.get(assumption1);
peps.add(psParameter.getSearchEngineProbability());
break;
}
}
if (!found2) {
ArrayList<Double> peps = new ArrayList<Double>(1);
assumptionPEPs.put(peptideAssumption, peps);
psParameter = (PSParameter) assumption.getUrParam(psParameter);
peps.add(psParameter.getSearchEngineProbability());
}
}
}
}
if (found) {
break;
}
}
}
Double bestSeP = null;
int nSe = -1;
for (PeptideAssumption peptideAssumption : assumptionPEPs.keySet()) {
ArrayList<Double> peps = assumptionPEPs.get(peptideAssumption);
Double sep = Collections.min(peps);
if (bestSeP == null || bestSeP > sep) {
bestSeP = sep;
nSe = peps.size();
bestPeptideAssumption = peptideAssumption;
} else if (peps.size() > nSe) {
if (sep != null && (Math.abs(sep - bestSeP) <= 1e-10)) {
nSe = peps.size();
bestPeptideAssumption = peptideAssumption;
}
}
}
}
// create a PeptideShaker match based on the best search engine match
Peptide sePeptide = bestPeptideAssumption.getPeptide();
ArrayList<String> psProteins =
new ArrayList<String>(sePeptide.getParentProteins(sequenceMatchingPreferences));
ArrayList<ModificationMatch> psModificationMatches = null;
if (sePeptide.isModified()) {
psModificationMatches =
new ArrayList<ModificationMatch>(sePeptide.getNModifications());
for (ModificationMatch seModMatch : sePeptide.getModificationMatches()) {
psModificationMatches.add(
new ModificationMatch(
seModMatch.getTheoreticPtm(),
seModMatch.isVariable(),
seModMatch.getModificationSite()));
}
}
Peptide psPeptide = new Peptide(sePeptide.getSequence(), psModificationMatches);
psPeptide.setParentProteins(psProteins);
PeptideAssumption psAssumption =
new PeptideAssumption(
psPeptide,
1,
Advocate.peptideShaker.getIndex(),
bestPeptideAssumption.getIdentificationCharge(),
retainedP);
spectrumMatch.setBestPeptideAssumption(psAssumption);
if (orderedPsmMap != null) {
String peptideKey = psPeptide.getMatchingKey(sequenceMatchingPreferences);
ArrayList<String> spectrumKeys = keysMap.get(peptideKey);
if (spectrumKeys == null) {
spectrumKeys = new ArrayList<String>();
keysMap.put(peptideKey, spectrumKeys);
}
spectrumKeys.add(spectrumKey);
}
psParameter = new PSParameter();
psParameter.setSpectrumProbabilityScore(retainedP);
PSParameter matchParameter =
(PSParameter) bestPeptideAssumption.getUrParam(psParameter);
psParameter.setSearchEngineProbability(matchParameter.getSearchEngineProbability());
psParameter.setAlgorithmDeltaPEP(matchParameter.getAlgorithmDeltaPEP());
psParameter.setDeltaPEP(matchParameter.getDeltaPEP());
matchesValidator
.getPsmMap()
.addPoint(
psParameter.getPsmProbabilityScore(),
spectrumMatch,
sequenceMatchingPreferences);
psParameter.setSpecificMapKey(
spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value + "");
identification.addSpectrumMatchParameter(spectrumKey, psParameter);
identification.updateSpectrumMatch(spectrumMatch);
}
}
if (!tagAssumptions.isEmpty()) {
ArrayList<Double> evalues = new ArrayList<Double>(tagAssumptions.keySet());
Double bestEvalue = Collections.min(evalues);
TagAssumption bestAssumption = tagAssumptions.get(bestEvalue).get(0);
spectrumMatch.setBestTagAssumption(bestAssumption);
identification.updateSpectrumMatch(spectrumMatch);
if (spectrumMatch.getBestPeptideAssumption() == null) {
psParameter = new PSParameter();
if (!multiSE) {
psParameter.setSpectrumProbabilityScore(bestEvalue);
}
PSParameter matchParameter = (PSParameter) bestAssumption.getUrParam(psParameter);
psParameter.setSearchEngineProbability(matchParameter.getSearchEngineProbability());
psParameter.setAlgorithmDeltaPEP(matchParameter.getAlgorithmDeltaPEP());
psParameter.setDeltaPEP(matchParameter.getDeltaPEP());
psParameter.setSpecificMapKey(
spectrumMatch.getBestTagAssumption().getIdentificationCharge().value + "");
identification.addSpectrumMatchParameter(spectrumKey, psParameter);
}
}
waitingHandler.increaseSecondaryProgressCounter();
if (waitingHandler.isRunCanceled()) {
return;
}
}
if (orderedPsmMap != null) {
ArrayList<String> orderedKeys =
new ArrayList<String>(
identification.getSpectrumIdentification(spectrumFileName).size());
for (ArrayList<String> keys : keysMap.values()) {
orderedKeys.addAll(keys);
}
orderedPsmMap.put(spectrumFileName, orderedKeys);
if (MemoryConsumptionStatus.memoryUsed() > 0.9) {
orderedPsmMap = null;
}
}
}
if (orderedPsmMap != null) {
metrics.setOrderedSpectrumKeys(orderedPsmMap);
}
// the protein count map is no longer needed
proteinCount.clear();
waitingHandler.setSecondaryProgressCounterIndeterminate(true);
}
/**
* Selects a first hit in a list of equally scoring peptide matches. The selection is made based
* on: 1 - The occurrence of the protein detection as given in the proteinCount map 2 - The
* sequence coverage by fragment ions 3 - The precursor mass error.
*
* <p>If no best hit is found, the first one sorted alphabetically is retained.
*
* @param spectrumKey the key of the spectrum
* @param firstHits list of equally scoring peptide matches
* @param proteinCount map of the number of peptides for every protein
* @param sequenceMatchingPreferences the sequence matching preferences
* @param shotgunProtocol the shotgun protocol
* @param identificationParameters the identification parameters
* @param spectrumAnnotator the spectrum annotator to use
* @return a first hit from the list of equally scoring peptide matches
* @throws IOException exception thrown whenever an IO exception occurred while remapping the
* proteins or getting the spectrum
* @throws InterruptedException exception thrown whenever an interrupted exception occurred while
* remapping the proteins or getting the spectrum
* @throws SQLException exception thrown whenever an SQL exception occurred while interacting with
* the protein tree
* @throws ClassNotFoundException exception thrown whenever an exception occurred while
* deserializing an object
* @throws MzMLUnmarshallerException exception thrown whenever an exception occurred while reading
* an mzML file
*/
public static PeptideAssumption getBestHit(
String spectrumKey,
ArrayList<PeptideAssumption> firstHits,
HashMap<String, Integer> proteinCount,
SequenceMatchingPreferences sequenceMatchingPreferences,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
PeptideSpectrumAnnotator spectrumAnnotator)
throws IOException, InterruptedException, SQLException, ClassNotFoundException,
MzMLUnmarshallerException {
if (firstHits.size() == 1) {
return firstHits.get(0);
}
Integer maxProteins = 0;
ArrayList<PeptideAssumption> bestPeptideAssumptions =
new ArrayList<PeptideAssumption>(firstHits.size());
for (PeptideAssumption peptideAssumption : firstHits) {
for (String accession :
peptideAssumption.getPeptide().getParentProteins(sequenceMatchingPreferences)) {
Integer count = proteinCount.get(accession);
if (count != null) {
if (count > maxProteins) {
maxProteins = count;
bestPeptideAssumptions.clear();
bestPeptideAssumptions.add(peptideAssumption);
} else if (count.equals(maxProteins)) {
bestPeptideAssumptions.add(peptideAssumption);
}
}
}
}
if (bestPeptideAssumptions.size() == 1) {
return bestPeptideAssumptions.get(0);
} else if (!bestPeptideAssumptions.isEmpty()) {
firstHits = bestPeptideAssumptions;
bestPeptideAssumptions = new ArrayList<PeptideAssumption>(firstHits.size());
}
MSnSpectrum spectrum = (MSnSpectrum) SpectrumFactory.getInstance().getSpectrum(spectrumKey);
int maxCoveredAminoAcids = 0;
AnnotationSettings annotationPreferences = identificationParameters.getAnnotationPreferences();
for (PeptideAssumption peptideAssumption : firstHits) {
Peptide peptide = peptideAssumption.getPeptide();
SpecificAnnotationSettings specificAnnotationPreferences =
annotationPreferences.getSpecificAnnotationPreferences(
spectrum.getSpectrumKey(),
peptideAssumption,
identificationParameters.getSequenceMatchingPreferences(),
identificationParameters.getPtmScoringPreferences().getSequenceMatchingPreferences());
HashMap<Integer, ArrayList<IonMatch>> coveredAminoAcids =
spectrumAnnotator.getCoveredAminoAcids(
annotationPreferences,
specificAnnotationPreferences,
(MSnSpectrum) spectrum,
peptide);
int nAas = coveredAminoAcids.size();
if (nAas > maxCoveredAminoAcids) {
maxCoveredAminoAcids = nAas;
bestPeptideAssumptions.clear();
bestPeptideAssumptions.add(peptideAssumption);
} else if (nAas == maxCoveredAminoAcids) {
bestPeptideAssumptions.add(peptideAssumption);
}
}
if (bestPeptideAssumptions.size() == 1) {
return bestPeptideAssumptions.get(0);
} else if (!bestPeptideAssumptions.isEmpty()) {
firstHits = bestPeptideAssumptions;
bestPeptideAssumptions = new ArrayList<PeptideAssumption>(firstHits.size());
}
double minMassError = identificationParameters.getPeptideAssumptionFilter().getMaxMzDeviation();
if (minMassError == -1.0) {
minMassError = identificationParameters.getSearchParameters().getPrecursorAccuracy();
}
for (PeptideAssumption peptideAssumption : firstHits) {
double massError =
Math.abs(
peptideAssumption.getDeltaMass(
spectrum.getPrecursor().getMz(), shotgunProtocol.isMs1ResolutionPpm()));
if (massError < minMassError) {
minMassError = massError;
bestPeptideAssumptions.clear();
bestPeptideAssumptions.add(peptideAssumption);
} else if (massError == minMassError) {
bestPeptideAssumptions.add(peptideAssumption);
}
}
if (bestPeptideAssumptions.size() == 1) {
return bestPeptideAssumptions.get(0);
} else if (bestPeptideAssumptions.isEmpty()) {
bestPeptideAssumptions = firstHits;
}
HashMap<String, PeptideAssumption> sequenceToPeptideAssumptionsMap =
new HashMap<String, PeptideAssumption>(bestPeptideAssumptions.size());
for (PeptideAssumption peptideAssumption : bestPeptideAssumptions) {
sequenceToPeptideAssumptionsMap.put(
peptideAssumption.getPeptide().getSequence(), peptideAssumption);
}
ArrayList<String> sequences = new ArrayList<String>(sequenceToPeptideAssumptionsMap.keySet());
Collections.sort(sequences);
return sequenceToPeptideAssumptionsMap.get(sequences.get(0));
}
}
public class PSFileImporter {
private File currentPSFile;
private EnzymeFactory enzymeFactory = EnzymeFactory.getInstance();
private String resource;
/** The spectrum annotator. */
private SpectrumAnnotator spectrumAnnotator = new SpectrumAnnotator();
/** The project details. */
private ProjectDetails projectDetails = null;
/** The spectrum factory. */
private SpectrumFactory spectrumFactory = SpectrumFactory.getInstance(100);
/** The identification to display. */
private Identification identification;
/** The compomics PTM factory. */
private PTMFactory ptmFactory = PTMFactory.getInstance();
/** The parameters of the search. */
private SearchParameters searchParameters = new SearchParameters();
/** The initial processing preferences */
private ProcessingPreferences processingPreferences = new ProcessingPreferences();
/** The annotation preferences. */
private AnnotationPreferences annotationPreferences = new AnnotationPreferences();
/** The spectrum counting preferences. */
private SpectrumCountingPreferences spectrumCountingPreferences =
new SpectrumCountingPreferences();
/** The PTM scoring preferences */
private PTMScoringPreferences ptmScoringPreferences = new PTMScoringPreferences();
/** The identification filter used for this project. */
private IdFilter idFilter = new IdFilter();
/** The actually identified modifications. */
/**
* Returns the modifications found in this project.
*
* @return the modifications found in this project
*/
public ArrayList<String> getFoundModifications() {
if (identifiedModifications == null) {
identifiedModifications = new ArrayList<String>();
for (String peptideKey : identification.getPeptideIdentification()) {
boolean modified = false;
for (String modificationName : Peptide.getModificationFamily(peptideKey)) {
if (!identifiedModifications.contains(modificationName)) {
identifiedModifications.add(modificationName);
modified = true;
}
}
if (!modified && !identifiedModifications.contains(PtmPanel.NO_MODIFICATION)) {
identifiedModifications.add(PtmPanel.NO_MODIFICATION);
}
}
}
return identifiedModifications;
}
private ArrayList<String> identifiedModifications = null;
/** Metrics picked-up while loading the files. */
private Metrics metrics;
/** The display preferences. */
private DisplayPreferences displayPreferences = new DisplayPreferences();
/** The sequence factory. */
private SequenceFactory sequenceFactory = SequenceFactory.getInstance(30000);
/** The filter preferences. */
private FilterPreferences filterPreferences = new FilterPreferences();
/** The compomics experiment. */
private MsExperiment experiment = null;
/** The investigated sample. */
private Sample sample;
/** The replicate number. */
private int replicateNumber;
/** The class used to provide sexy features out of the identification. */
private IdentificationFeaturesGenerator identificationFeaturesGenerator;
/** The last folder opened by the user. Defaults to user.home. */
private String lastSelectedFolder = "user.home";
/** The object cache used for the identification database. */
private ObjectsCache objectsCache;
private com.compomics.util.experiment.ProteomicAnalysis proteomicAnalysis;
private ProgressDialogX progressDialog;
private javax.swing.JProgressBar jprog;
public PSFileImporter(javax.swing.JProgressBar jprog) {
this.progressDialog = new ProgressDialogX(false);
this.jprog = jprog;
}
public void importPeptideShakerFile(File aPsFile, final String resource) {
this.resource = resource;
this.currentPSFile = aPsFile;
loadGeneMapping();
loadEnzymes();
resetPtmFactory();
// setDefaultPreferences(); // @TODO: i tried re-adding this but then we get a null pointer, but
// the two below have to be added or the default neutral losses won't appear
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.H2O);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3);
// exceptionHandler = new ExceptionHandler(this);
new Thread("ProgressThread") {
@Override
public void run() {
jprog.setValue(10);
}
}.start();
Thread importThread =
new Thread("ImportThread") {
@Override
public void run() {
try {
// reset enzymes, ptms and preferences
loadEnzymes();
resetPtmFactory();
setDefaultPreferences();
try {
// close any open connection to an identification database
if (identification != null) {
identification.close();
}
} catch (Exception e) {
e.printStackTrace();
}
File experimentFile =
new File(
PeptideShaker.SERIALIZATION_DIRECTORY, PeptideShaker.experimentObjectName);
File matchFolder = new File(PeptideShaker.SERIALIZATION_DIRECTORY);
// empty the existing files in the matches folder
if (matchFolder.exists()) {
for (File file : matchFolder.listFiles()) {
if (file.isDirectory()) {
boolean deleted = Util.deleteDir(file);
if (!deleted) {
System.out.println("Failed to delete folder: " + file.getPath());
}
} else {
boolean deleted = file.delete();
if (!deleted) {
System.out.println("Failed to delete file: " + file.getPath());
}
}
}
}
final int BUFFER = 2048;
byte data[] = new byte[BUFFER];
FileInputStream fi = new FileInputStream(currentPSFile);
BufferedInputStream bis = new BufferedInputStream(fi, BUFFER);
try {
ArchiveInputStream tarInput =
new ArchiveStreamFactory().createArchiveInputStream(bis);
ArchiveEntry archiveEntry;
while ((archiveEntry = tarInput.getNextEntry()) != null) {
File destinationFile = new File(archiveEntry.getName());
File destinationFolder = destinationFile.getParentFile();
boolean destFolderExists = true;
if (!destinationFolder.exists()) {
destFolderExists = destinationFolder.mkdirs();
}
if (destFolderExists) {
FileOutputStream fos = new FileOutputStream(destinationFile);
BufferedOutputStream bos = new BufferedOutputStream(fos);
int count;
while ((count = tarInput.read(data, 0, BUFFER)) != -1
&& !progressDialog.isRunCanceled()) {
bos.write(data, 0, count);
}
bos.close();
fos.close();
// int progress = (int) (100 *
// tarInput.getBytesRead() / fileLength);
// progressDialog.setValue(progress);
} else {
System.out.println(
"Folder does not exist: \'"
+ destinationFolder.getAbsolutePath()
+ "\'. User preferences not saved.");
}
}
tarInput.close();
} catch (ArchiveException e) {
// Most likely an old project
experimentFile = currentPSFile;
e.printStackTrace();
}
fi.close();
bis.close();
fi.close();
MsExperiment tempExperiment = ExperimentIO.loadExperiment(experimentFile);
Sample tempSample = null;
PeptideShakerSettings experimentSettings = new PeptideShakerSettings();
if (tempExperiment.getUrParam(experimentSettings) instanceof PSSettings) {
// convert old settings files using utilities version 3.10.68 or older
// convert the old ProcessingPreferences object
PSSettings tempSettings =
(PSSettings) tempExperiment.getUrParam(experimentSettings);
ProcessingPreferences tempProcessingPreferences = new ProcessingPreferences();
tempProcessingPreferences.setProteinFDR(
tempSettings.getProcessingPreferences().getProteinFDR());
tempProcessingPreferences.setPeptideFDR(
tempSettings.getProcessingPreferences().getPeptideFDR());
tempProcessingPreferences.setPsmFDR(
tempSettings.getProcessingPreferences().getPsmFDR());
// convert the old PTMScoringPreferences object
PTMScoringPreferences tempPTMScoringPreferences = new PTMScoringPreferences();
tempPTMScoringPreferences.setaScoreCalculation(
tempSettings.getPTMScoringPreferences().aScoreCalculation());
tempPTMScoringPreferences.setaScoreNeutralLosses(
tempSettings.getPTMScoringPreferences().isaScoreNeutralLosses());
tempPTMScoringPreferences.setFlrThreshold(
tempSettings.getPTMScoringPreferences().getFlrThreshold());
// missing gene refrences
GenePreferences genePreferences = getGenePreferences();
// String selectedSpecies = genePreferences.getCurrentSpecies();
// String speciesDatabase =
// genePreferences.getEnsemblDatabaseName(selectedSpecies);
experimentSettings =
new PeptideShakerSettings(
tempSettings.getSearchParameters(),
tempSettings.getAnnotationPreferences(),
tempSettings.getSpectrumCountingPreferences(),
tempSettings.getProjectDetails(),
tempSettings.getFilterPreferences(),
tempSettings.getDisplayPreferences(),
tempSettings.getMetrics(),
tempProcessingPreferences,
tempSettings.getIdentificationFeaturesCache(),
tempPTMScoringPreferences,
genePreferences,
new IdFilter());
;
} else {
experimentSettings =
(PeptideShakerSettings) tempExperiment.getUrParam(experimentSettings);
}
idFilter = experimentSettings.getIdFilter();
setAnnotationPreferences(experimentSettings.getAnnotationPreferences());
setSpectrumCountingPreferences(experimentSettings.getSpectrumCountingPreferences());
setPtmScoringPreferences(experimentSettings.getPTMScoringPreferences());
setProjectDetails(experimentSettings.getProjectDetails());
setSearchParameters(experimentSettings.getSearchParameters());
setProcessingPreferences(experimentSettings.getProcessingPreferences());
setMetrics(experimentSettings.getMetrics());
setDisplayPreferences(experimentSettings.getDisplayPreferences());
if (experimentSettings.getFilterPreferences() != null) {
setFilterPreferences(experimentSettings.getFilterPreferences());
} else {
setFilterPreferences(new FilterPreferences());
}
if (experimentSettings.getDisplayPreferences() != null) {
setDisplayPreferences(experimentSettings.getDisplayPreferences());
displayPreferences.compatibilityCheck(searchParameters.getModificationProfile());
} else {
setDisplayPreferences(new DisplayPreferences());
displayPreferences.setDefaultSelection(searchParameters.getModificationProfile());
}
ArrayList<Sample> samples = new ArrayList(tempExperiment.getSamples().values());
if (samples.size() == 1) {
tempSample = samples.get(0);
} else {
tempSample = samples.get(0);
String[] sampleNames = new String[samples.size()];
for (int cpt = 0; cpt < sampleNames.length; cpt++) {
sampleNames[cpt] = samples.get(cpt).getReference();
System.out.println(sampleNames[cpt]);
}
SampleSelection sampleSelection =
new SampleSelection(null, true, sampleNames, "sample");
sampleSelection.setVisible(false);
String choice = sampleSelection.getChoice();
for (Sample sampleTemp : samples) {
if (sampleTemp.getReference().equals(choice)) {
tempSample = sampleTemp;
break;
}
}
}
ArrayList<Integer> replicates =
new ArrayList(tempExperiment.getAnalysisSet(tempSample).getReplicateNumberList());
System.out.println(replicates);
int tempReplicate;
if (replicates.size() == 1) {
tempReplicate = replicates.get(0);
} else {
String[] replicateNames = new String[replicates.size()];
for (int cpt = 0; cpt < replicateNames.length; cpt++) {
replicateNames[cpt] = samples.get(cpt).getReference();
}
SampleSelection sampleSelection =
new SampleSelection(null, true, replicateNames, "replicate");
sampleSelection.setVisible(false);
Integer choice = new Integer(sampleSelection.getChoice());
tempReplicate = 0;
}
setProject(tempExperiment, tempSample, tempReplicate);
identificationFeaturesGenerator =
new IdentificationFeaturesGenerator(
identification,
searchParameters,
idFilter,
metrics,
spectrumCountingPreferences);
if (experimentSettings.getIdentificationFeaturesCache() != null) {
identificationFeaturesGenerator.setIdentificationFeaturesCache(
experimentSettings.getIdentificationFeaturesCache());
}
// mainProgressDialog.setTitle("Loading FASTA File. Please
// Wait...");
try {
File providedFastaLocation =
experimentSettings.getSearchParameters().getFastaFile();
String fileName = providedFastaLocation.getName();
File projectFolder = currentPSFile.getParentFile();
File dataFolder = new File(projectFolder, "data");
// try to locate the FASTA file
if (providedFastaLocation.exists()) {
SequenceFactory.getInstance().loadFastaFile(providedFastaLocation);
} else if (new File(projectFolder, fileName).exists()) {
SequenceFactory.getInstance().loadFastaFile(new File(projectFolder, fileName));
experimentSettings
.getSearchParameters()
.setFastaFile(new File(projectFolder, fileName));
} else if (new File(dataFolder, fileName).exists()) {
SequenceFactory.getInstance().loadFastaFile(new File(dataFolder, fileName));
experimentSettings
.getSearchParameters()
.setFastaFile(new File(dataFolder, fileName));
} else {
// return error
System.out.println("fastafile is missing");
}
} catch (Exception e) {
e.printStackTrace();
System.out.println("fastafile is missing");
}
// mainProgressDialog.setTitle("Locating Spectrum Files. Please
// Wait...");
for (String spectrumFileName : identification.getSpectrumFiles()) {
try {
File providedSpectrumLocation = projectDetails.getSpectrumFile(spectrumFileName);
// try to locate the spectrum file
if (providedSpectrumLocation == null || !providedSpectrumLocation.exists()) {
File projectFolder = currentPSFile.getParentFile();
File fileInProjectFolder = new File(projectFolder, spectrumFileName);
File dataFolder = new File(projectFolder, "data");
File fileInDataFolder = new File(dataFolder, spectrumFileName);
File fileInLastSelectedFolder =
new File(getLastSelectedFolder(), spectrumFileName);
if (fileInProjectFolder.exists()) {
projectDetails.addSpectrumFile(fileInProjectFolder);
} else if (fileInDataFolder.exists()) {
projectDetails.addSpectrumFile(fileInDataFolder);
} else if (fileInLastSelectedFolder.exists()) {
projectDetails.addSpectrumFile(fileInLastSelectedFolder);
} else {
System.out.println("error no file");
}
}
} catch (Exception e) {
clearData(true);
// clearPreferences();
e.printStackTrace();
System.out.println("error no file");
return;
}
}
objectsCache = new ObjectsCache();
objectsCache.setAutomatedMemoryManagement(true);
if (identification.isDB()) {
try {
String dbFolder =
new File(resource, PeptideShaker.SERIALIZATION_DIRECTORY).getAbsolutePath();
identification.establishConnection(dbFolder, false, objectsCache);
} catch (Exception e) {
e.printStackTrace();
}
} else {
updateAnnotationPreferencesFromSearchSettings();
annotationPreferences.useAutomaticAnnotation(true);
}
int cpt = 1, nfiles = identification.getSpectrumFiles().size();
for (String fileName : identification.getSpectrumFiles()) {
// mainProgressDialog.setTitle("Importing Spectrum
// Files. Please Wait...");
try {
File mgfFile = projectDetails.getSpectrumFile(fileName);
spectrumFactory.addSpectra(mgfFile, progressDialog);
} catch (Exception e) {
clearData(true);
e.printStackTrace();
return;
}
}
boolean compatibilityIssue =
getSearchParameters().getIonSearched1() == null
|| getSearchParameters().getIonSearched2() == null;
if (compatibilityIssue) {
JOptionPane.showMessageDialog(
null,
"The annotation preferences for this project may have changed.\n\n"
+ "Note that PeptideShaker has substancially improved, we strongly\n"
+ "recommend reprocessing your identification files.",
"Annotation Preferences",
JOptionPane.INFORMATION_MESSAGE);
updateAnnotationPreferencesFromSearchSettings();
}
if (identification.getSpectrumIdentificationMap() == null) {
// 0.18 version, needs update of the spectrum mapping
identification.updateSpectrumMapping();
}
} catch (OutOfMemoryError error) {
System.out.println(
"Ran out of memory! (runtime.maxMemory(): "
+ Runtime.getRuntime().maxMemory()
+ ")");
Runtime.getRuntime().gc();
JOptionPane.showMessageDialog(
null,
"The task used up all the available memory and had to be stopped.\n"
+ "Memory boundaries are set in ../resources/conf/JavaOptions.txt.",
"Out Of Memory Error",
JOptionPane.ERROR_MESSAGE);
error.printStackTrace();
} catch (Exception exp) {
exp.printStackTrace();
}
}
};
importThread.setPriority(Thread.MAX_PRIORITY);
// importThread.start();
// while (importThread.isAlive()) {
// try {
// Thread.currentThread().sleep(100);
//
// } catch (Exception e) {
// e.printStackTrace();
// }
// }
ExecutorService es = Executors.newCachedThreadPool();
es.execute(importThread);
es.shutdown();
try {
boolean finshed = es.awaitTermination(1, TimeUnit.DAYS);
System.gc();
return;
// t.start();
} catch (InterruptedException ex) {
System.err.println(ex.getMessage());
// Logger.getLogger(UpdatedOutputGenerator.class.getName()).log(Level.SEVERE, null, ex);
}
System.gc();
// return;
}
/** Loads the enzymes from the enzyme file into the enzyme factory. */
private void loadEnzymes() {
try {
enzymeFactory.importEnzymes(new File(resource, PeptideShaker.ENZYME_FILE));
} catch (Exception e) {
System.out.println("Not able to load the enzyme file." + "Wrong enzyme file.");
e.printStackTrace();
}
}
/** Loads the modifications from the modification file. */
public void resetPtmFactory() {
// reset ptm factory
ptmFactory.reloadFactory();
ptmFactory = PTMFactory.getInstance();
try {
ptmFactory.importModifications(new File(resource, PeptideShaker.MODIFICATIONS_FILE), false);
} catch (Exception e) {
e.printStackTrace();
}
try {
ptmFactory.importModifications(
new File(resource, PeptideShaker.USER_MODIFICATIONS_FILE), true);
} catch (Exception e) {
e.printStackTrace();
}
}
/** Set the default preferences. */
private void setDefaultPreferences() {
searchParameters = new SearchParameters();
annotationPreferences.setAnnotationLevel(0.75);
annotationPreferences.useAutomaticAnnotation(true);
spectrumCountingPreferences.setSelectedMethod(SpectralCountingMethod.NSAF);
spectrumCountingPreferences.setValidatedHits(true);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.H2O);
processingPreferences = new ProcessingPreferences();
ptmScoringPreferences = new PTMScoringPreferences();
}
/** Imports the gene mapping. */
private void loadGeneMapping() {
try {
geneFactory.initialize(new File(resource, GENE_MAPPING_PATH), null);
} catch (Exception e) {
e.printStackTrace();
}
}
/** The path to the gene mapping file. */
private final String GENE_MAPPING_PATH = "/resources/conf/gene_ontology/gene_details_human";
/** The gene factory. */
private GeneFactory geneFactory = GeneFactory.getInstance();
/**
* Updates the new annotation preferences.
*
* @param annotationPreferences the new annotation preferences
*/
public void setAnnotationPreferences(AnnotationPreferences annotationPreferences) {
this.annotationPreferences = annotationPreferences;
}
/**
* Sets new spectrum counting preferences.
*
* @param spectrumCountingPreferences new spectrum counting preferences
*/
public void setSpectrumCountingPreferences(
SpectrumCountingPreferences spectrumCountingPreferences) {
this.spectrumCountingPreferences = spectrumCountingPreferences;
}
/**
* Sets the PTM scoring preferences
*
* @param ptmScoringPreferences the PTM scoring preferences
*/
public void setPtmScoringPreferences(PTMScoringPreferences ptmScoringPreferences) {
this.ptmScoringPreferences = ptmScoringPreferences;
}
/**
* Sets the project details.
*
* @param projectDetails the project details
*/
public void setProjectDetails(ProjectDetails projectDetails) {
this.projectDetails = projectDetails;
}
/**
* Updates the search parameters.
*
* @param searchParameters the new search parameters
*/
public void setSearchParameters(SearchParameters searchParameters) {
this.searchParameters = searchParameters;
PeptideShaker.loadModifications(searchParameters);
}
/**
* Sets the initial processing preferences.
*
* @param processingPreferences the initial processing preferences
*/
public void setProcessingPreferences(ProcessingPreferences processingPreferences) {
this.processingPreferences = processingPreferences;
}
/**
* Sets the metrics saved while loading the files.
*
* @param metrics the metrics saved while loading the files
*/
public void setMetrics(Metrics metrics) {
this.metrics = metrics;
}
/**
* Sets the display preferences to use.
*
* @param displayPreferences the display preferences to use
*/
public void setDisplayPreferences(DisplayPreferences displayPreferences) {
this.displayPreferences = displayPreferences;
}
/**
* Sets the gui filter preferences to use. .\
*
* @param filterPreferences the gui filter preferences to use
*/
public void setFilterPreferences(FilterPreferences filterPreferences) {
this.filterPreferences = filterPreferences;
}
/**
* This method sets the information of the project when opened.
*
* @param experiment the experiment conducted
* @param sample The sample analyzed
* @param replicateNumber The replicate number
*/
public void setProject(MsExperiment experiment, Sample sample, int replicateNumber) {
this.experiment = experiment;
this.sample = sample;
this.replicateNumber = replicateNumber;
ProteomicAnalysis proteomic_Analysis =
experiment.getAnalysisSet(sample).getProteomicAnalysis(replicateNumber);
identification = proteomic_Analysis.getIdentification(IdentificationMethod.MS2_IDENTIFICATION);
}
/**
* Returns the last selected folder.
*
* @return the last selected folder
*/
public String getLastSelectedFolder() {
return lastSelectedFolder;
}
/**
* Set the last selected folder.
*
* @param lastSelectedFolder the folder to set
*/
public void setLastSelectedFolder(String lastSelectedFolder) {
this.lastSelectedFolder = lastSelectedFolder;
}
/**
* Returns the identification displayed.
*
* @return the identification displayed
*/
public com.compomics.util.experiment.identification.Identification getIdentification() {
return identification;
}
/**
* Returns the identification features generator.
*
* @return the identification features generator
*/
public IdentificationFeaturesGenerator getIdentificationFeaturesGenerator() {
return identificationFeaturesGenerator;
}
/**
* Returns the search parameters.
*
* @return the search parameters
*/
public SearchParameters getSearchParameters() {
return searchParameters;
}
/**
* Return the display preferences to use.
*
* @return the display preferences to use
*/
public DisplayPreferences getDisplayPreferences() {
return displayPreferences;
}
public ArrayList<IonMatch> getIonsCurrentlyMatched() throws MzMLUnmarshallerException {
return spectrumAnnotator.getCurrentAnnotation(
annotationPreferences.getIonTypes(),
annotationPreferences.getNeutralLosses(),
annotationPreferences.getValidatedCharges());
}
public SpectrumAnnotator getSpectrumAnnorator() {
return spectrumAnnotator;
}
public void clearData(boolean clearDatabaseFolder) {
projectDetails = null;
spectrumAnnotator = new SpectrumAnnotator();
try {
spectrumFactory.closeFiles();
} catch (Exception e) {
e.printStackTrace();
}
try {
sequenceFactory.closeFile();
} catch (Exception e) {
e.printStackTrace();
}
try {
GOFactory.getInstance().closeFiles();
} catch (Exception e) {
e.printStackTrace();
}
try {
spectrumFactory.clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
try {
sequenceFactory.clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
try {
GOFactory.getInstance().clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
identifiedModifications = null;
if (clearDatabaseFolder) {
clearDatabaseFolder();
}
resetFeatureGenerator();
// set up the tabs/panels
currentPSFile = null;
}
/** Resets the feature generator. */
public void resetFeatureGenerator() {
identificationFeaturesGenerator =
new IdentificationFeaturesGenerator(
identification, searchParameters, idFilter, metrics, spectrumCountingPreferences);
}
/** Clears the database folder. */
private void clearDatabaseFolder() {
boolean databaseClosed = true;
// close the database connection
if (identification != null) {
try {
identification.close();
identification = null;
} catch (SQLException e) {
databaseClosed = false;
e.printStackTrace();
JOptionPane.showMessageDialog(
null, "Failed to close the database.", "Database Error", JOptionPane.WARNING_MESSAGE);
}
}
// empty the matches folder
if (databaseClosed) {
File matchFolder = new File(resource, PeptideShaker.SERIALIZATION_DIRECTORY);
if (matchFolder.exists()) {
File[] tempFiles = matchFolder.listFiles();
if (tempFiles != null) {
for (File currentFile : tempFiles) {
Util.deleteDir(currentFile);
}
}
if (matchFolder.listFiles() != null && matchFolder.listFiles().length > 0) {
JOptionPane.showMessageDialog(
null,
"Failed to empty the database folder:\n" + matchFolder.getPath() + ".",
"Database Cleanup Failed",
JOptionPane.WARNING_MESSAGE);
}
}
}
}
/** Updates the ions used for fragment annotation. */
public void updateAnnotationPreferencesFromSearchSettings() {
annotationPreferences.setPreferencesFromSearchParamaers(searchParameters);
}
/**
* Returns the gene preferences.
*
* @return the gene preferences
*/
public GenePreferences getGenePreferences() {
return genePreferences;
}
private GenePreferences genePreferences = new GenePreferences();
/**
* Returns the experiment.
*
* @return the experiment
*/
public MsExperiment getExperiment() {
return experiment;
}
/*
* Returns the sample.
* @return the sample
*/
public Sample getSample() {
return sample;
}
/**
* Returns the replicate number.
*
* @return the replicateNumber
*/
public int getReplicateNumber() {
return this.replicateNumber;
}
/**
* Returns the desired spectrum.
*
* @param spectrumKey the key of the spectrum
* @return the desired spectrum
*/
public MSnSpectrum getSpectrum(String spectrumKey) {
String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
String spectrumTitle = Spectrum.getSpectrumTitle(spectrumKey);
try {
return (MSnSpectrum) spectrumFactory.getSpectrum(spectrumFile, spectrumTitle);
} catch (Exception e) {
System.out.println(e.getMessage());
return null;
}
}
}
/**
* Indicates whether the match designated by the match key validates the given item using the
* given comparator and value threshold.
*
* @param itemName the name of the item to filter on
* @param filterItemComparator the comparator to use
* @param value the value to use as a threshold
* @param spectrumKey the key of the match of interest
* @param peptideAssumption the assumption to validate
* @param identification the identification objects where to get identification matches from
* @param identificationFeaturesGenerator the identification feature generator where to get
* identification features
* @param identificationParameters the identification parameters used
* @param peptideSpectrumAnnotator the annotator to use to annotate spectra when filtering on PSM
* or assumptions
* @return a boolean indicating whether the match designated by the protein key validates the
* given item using the given comparator and value threshold.
* @throws java.io.IOException exception thrown whenever an exception occurred while reading or
* writing a file
* @throws java.lang.InterruptedException exception thrown whenever a threading issue occurred
* while validating that the match passes the filter
* @throws java.lang.ClassNotFoundException exception thrown whenever an error occurred while
* deserilalizing a match
* @throws java.sql.SQLException exception thrown whenever an error occurred while interacting
* with a database
* @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException exception thrown whenever an error
* occurred while reading an mzML file
* @throws org.apache.commons.math.MathException exception thrown whenever an error occurred while
* doing statistics on a distribution
*/
public boolean isValidated(
String itemName,
FilterItemComparator filterItemComparator,
Object value,
String spectrumKey,
PeptideAssumption peptideAssumption,
Identification identification,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
throws IOException, InterruptedException, ClassNotFoundException, SQLException,
MzMLUnmarshallerException, MathException {
AssumptionFilterItem filterItem = AssumptionFilterItem.getItem(itemName);
if (filterItem == null) {
throw new IllegalArgumentException(
"Filter item " + itemName + "not recognized as spectrum assumption filter item.");
}
String input = value.toString();
switch (filterItem) {
case precrusorMz:
Precursor precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
Double mz = precursor.getMz();
return filterItemComparator.passes(input, mz.toString());
case precrusorRT:
precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
Double rt = precursor.getRt();
return filterItemComparator.passes(input, rt.toString());
case precrusorCharge:
Integer charge = peptideAssumption.getIdentificationCharge().value;
return filterItemComparator.passes(input, charge.toString());
case precrusorMzErrorDa:
precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
SearchParameters searchParameters = identificationParameters.getSearchParameters();
Double mzError =
Math.abs(
peptideAssumption.getDeltaMass(
precursor.getMz(),
false,
searchParameters.getMinIsotopicCorrection(),
searchParameters.getMaxIsotopicCorrection()));
return filterItemComparator.passes(input, mzError.toString());
case precrusorMzErrorPpm:
searchParameters = identificationParameters.getSearchParameters();
precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
mzError =
Math.abs(
peptideAssumption.getDeltaMass(
precursor.getMz(),
true,
searchParameters.getMinIsotopicCorrection(),
searchParameters.getMaxIsotopicCorrection()));
return filterItemComparator.passes(input, mzError.toString());
case precrusorMzErrorStat:
searchParameters = identificationParameters.getSearchParameters();
precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
mzError =
peptideAssumption.getDeltaMass(
precursor.getMz(),
identificationParameters.getSearchParameters().isPrecursorAccuracyTypePpm(),
searchParameters.getMinIsotopicCorrection(),
searchParameters.getMaxIsotopicCorrection());
NonSymmetricalNormalDistribution precDeviationDistribution =
identificationFeaturesGenerator.getMassErrorDistribution(
Spectrum.getSpectrumFile(spectrumKey));
Double p;
if (mzError > precDeviationDistribution.getMean()) {
p = precDeviationDistribution.getDescendingCumulativeProbabilityAt(mzError);
} else {
p = precDeviationDistribution.getCumulativeProbabilityAt(mzError);
}
return filterItemComparator.passes(input, p.toString());
case sequenceCoverage:
SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
MSnSpectrum spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
Peptide peptide = peptideAssumption.getPeptide();
AnnotationSettings annotationPreferences =
identificationParameters.getAnnotationPreferences();
SpecificAnnotationSettings specificAnnotationPreferences =
annotationPreferences.getSpecificAnnotationPreferences(
spectrum.getSpectrumKey(),
peptideAssumption,
identificationParameters.getSequenceMatchingPreferences(),
identificationParameters
.getPtmScoringPreferences()
.getSequenceMatchingPreferences());
HashMap<Integer, ArrayList<IonMatch>> matches =
peptideSpectrumAnnotator.getCoveredAminoAcids(
annotationPreferences,
specificAnnotationPreferences,
(MSnSpectrum) spectrum,
peptide);
double nCovered = 0;
int nAA = peptide.getSequence().length();
for (int i = 0; i <= nAA; i++) {
ArrayList<IonMatch> matchesAtAa = matches.get(i);
if (matchesAtAa != null && !matchesAtAa.isEmpty()) {
nCovered++;
}
}
Double coverage = 100.0 * nCovered / nAA;
return filterItemComparator.passes(input, coverage.toString());
case algorithmScore:
Double score = peptideAssumption.getRawScore();
if (score == null) {
score = peptideAssumption.getScore();
}
return filterItemComparator.passes(input, score.toString());
case fileNames:
return filterItemComparator.passes(input, Spectrum.getSpectrumFile(spectrumKey));
case confidence:
PSParameter psParameter = new PSParameter();
psParameter =
(PSParameter) identification.getPeptideMatchParameter(spectrumKey, psParameter);
Double confidence = psParameter.getProteinConfidence();
return filterItemComparator.passes(input, confidence.toString());
case validationStatus:
psParameter = new PSParameter();
psParameter =
(PSParameter) identification.getPeptideMatchParameter(spectrumKey, psParameter);
Integer validation = psParameter.getMatchValidationLevel().getIndex();
return filterItemComparator.passes(input, validation.toString());
case stared:
psParameter = new PSParameter();
psParameter =
(PSParameter) identification.getPeptideMatchParameter(spectrumKey, psParameter);
String starred;
if (psParameter.isStarred()) {
starred = FilterItemComparator.trueFalse[0];
} else {
starred = FilterItemComparator.trueFalse[1];
}
return filterItemComparator.passes(input, starred);
default:
throw new IllegalArgumentException(
"Protein filter not implemented for item " + filterItem.name + ".");
}
}