/**
* Opens a file chooser for importing method settings.
*
* @param evt
*/
private void browseConfigButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_browseConfigButtonActionPerformed
if (txtConfigurationFileLocation.getText().length() > 0) {
newDialog
.getReporterGui()
.getLastSelectedFolder()
.setLastSelectedFolder(txtConfigurationFileLocation.getText());
}
File selectedFile =
Util.getUserSelectedFile(
this,
".xml",
"Reporter Method File (*.xml)",
"Select Settings File",
newDialog.getReporterGui().getLastSelectedFolder().getLastSelectedFolder(),
null,
true);
if (selectedFile != null) {
try {
methodsFactory.importMethods(selectedFile);
newDialog.setSelectedMethod(newDialog.getMethod(newDialog.getSelectedMethod().getName()));
newDialog.setReagents(newDialog.getSelectedMethod().getReagentsSortedByMass());
refresh();
txtConfigurationFileLocation.setText(selectedFile.getAbsolutePath());
newDialog.setMethodsFile(selectedFile);
newDialog
.getReporterGui()
.getLastSelectedFolder()
.setLastSelectedFolder(selectedFile.getPath());
} catch (IOException e) {
JOptionPane.showMessageDialog(
null,
"File " + selectedFile.getAbsolutePath() + " not found.",
"File Not Found",
JOptionPane.WARNING_MESSAGE);
} catch (XmlPullParserException e) {
JOptionPane.showMessageDialog(
null,
"An error occurred while parsing "
+ selectedFile.getAbsolutePath()
+ " at line "
+ e.getLineNumber()
+ ".",
"Parsing Error",
JOptionPane.WARNING_MESSAGE);
e.printStackTrace();
}
}
} // GEN-LAST:event_browseConfigButtonActionPerformed
/**
* Save the method settings.
*
* @param evt
*/
private void saveConfigButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_saveConfigButtonActionPerformed
String tempFileName = null;
if (txtConfigurationFileLocation.getText().length() > 0) {
newDialog
.getReporterGui()
.getLastSelectedFolder()
.setLastSelectedFolder(txtConfigurationFileLocation.getText());
tempFileName = new File(txtConfigurationFileLocation.getText()).getName();
}
File selectedFile =
Util.getUserSelectedFile(
this,
".xml",
"Reporter Method File (*.xml)",
"Save Settings File",
newDialog.getReporterGui().getLastSelectedFolder().getLastSelectedFolder(),
tempFileName,
false);
if (selectedFile != null) {
try {
methodsFactory.saveFile(selectedFile);
newDialog.setMethodsFile(selectedFile);
txtConfigurationFileLocation.setText(selectedFile.getAbsolutePath());
valuesChanged = false;
JOptionPane.showMessageDialog(
null,
"Settings saved to " + selectedFile.getAbsolutePath() + ".",
"Settings Saved",
JOptionPane.INFORMATION_MESSAGE);
} catch (IOException ex) {
JOptionPane.showMessageDialog(
null,
"An error occured when saving the file.",
"File Error",
JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
} // GEN-LAST:event_saveConfigButtonActionPerformed
/** 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);
}
}
}
}
/**
* Create the parameters file.
*
* @param searchParametersFile the file where to save the search parameters
* @return the parameters file
* @throws IOException exception thrown whenever an error occurred while writing the configuration
* file
*/
private File createParametersFile(File searchParametersFile) throws IOException {
File andromedaTempFolder = new File(andromedaTempFolderPath);
String fileName;
try {
fileName = Util.removeExtension(searchParametersFile.getName()) + ".apar";
} catch (Exception e) {
fileName = "SearchGUI.apar";
}
File parameterFile = new File(andromedaTempFolder, fileName);
BufferedWriter bw = new BufferedWriter(new FileWriter(parameterFile));
try {
boolean semiSpecific = false;
DigestionPreferences digestionPreferences = searchParameters.getDigestionPreferences();
if (digestionPreferences.getCleavagePreference()
== DigestionPreferences.CleavagePreference.enzyme) {
Enzyme enzyme = digestionPreferences.getEnzymes().get(0);
String enzymeName = enzyme.getName();
bw.write("enzymes=" + enzymeName); // @TODO: support multiple enzymes?
bw.newLine();
if (digestionPreferences.getSpecificity(enzyme.getName())
== DigestionPreferences.Specificity.semiSpecific
|| digestionPreferences.getSpecificity(enzyme.getName())
== DigestionPreferences.Specificity.specificCTermOnly
|| digestionPreferences.getSpecificity(enzyme.getName())
== DigestionPreferences.Specificity.specificNTermOnly) {
semiSpecific = true;
}
} else if (digestionPreferences.getCleavagePreference()
== DigestionPreferences.CleavagePreference.unSpecific) {
bw.write("enzyme mode=unspecific");
bw.newLine();
} else {
// whole enzyme
// @TODO: what to put here..?
}
if (semiSpecific) {
bw.write("enzyme mode=semispecific"); // @TODO: support: Semispecific Free N-terminus and
// Semispecific Free C-terminus
} else {
bw.write("enzyme mode=specific");
}
bw.newLine();
PtmSettings modificationProfile = searchParameters.getPtmSettings();
StringBuilder list = new StringBuilder();
for (String ptmName : modificationProfile.getVariableModifications()) {
if (list.length() > 0) {
list.append(",");
}
list.append(ptmName);
}
bw.write("variable modifications=" + list);
bw.newLine();
list = new StringBuilder();
for (String ptmName : modificationProfile.getFixedModifications()) {
if (list.length() > 0) {
list.append(",");
}
list.append(ptmName);
}
bw.write("fixed modifications=" + list);
bw.newLine();
bw.write("label modifications="); // @TODO: support labels
bw.newLine();
if (!modificationProfile.getRefinementVariableModifications().isEmpty()) {
bw.write("has additional variable modifications=True");
bw.newLine();
list = new StringBuilder();
for (String ptmName : modificationProfile.getRefinementVariableModifications()) {
if (list.length() > 0) {
list.append(",");
}
list.append(ptmName);
}
bw.write("additional variable modifications=" + list);
bw.newLine();
bw.write("additional variable modification proteins=");
bw.newLine();
} else {
bw.write("has additional variable modifications=False");
bw.newLine();
bw.write("additional variable modifications=");
bw.newLine();
bw.write("additional variable modification proteins=");
bw.newLine();
}
bw.write("peptide mass tolerance=" + searchParameters.getPrecursorAccuracy());
bw.newLine();
bw.write("max peptide mass=" + andromedaParameters.getMaxPeptideMass());
bw.newLine();
bw.write("max combinations=" + andromedaParameters.getMaxCombinations());
bw.newLine();
if (searchParameters.isPrecursorAccuracyTypePpm()) {
bw.write("peptide mass tolerance Unit=ppm");
} else {
bw.write("peptide mass tolerance Unit=Da");
}
bw.newLine();
bw.write("fragment mass tolerance=" + searchParameters.getFragmentIonAccuracy());
bw.newLine();
if (searchParameters.getFragmentAccuracyType() == SearchParameters.MassAccuracyType.PPM) {
bw.write("fragment mass tolerance Unit=ppm");
} else {
bw.write("fragment mass tolerance Unit=Da");
}
bw.newLine();
bw.write("top peaks=" + andromedaParameters.getTopPeaks());
bw.newLine();
bw.write("top peaks window=" + andromedaParameters.getTopPeaksWindow());
bw.newLine();
if (digestionPreferences.getCleavagePreference()
== DigestionPreferences.CleavagePreference.enzyme) {
Integer missedCleavages = null;
for (Enzyme enzyme : digestionPreferences.getEnzymes()) {
int enzymeMissedCleavages = digestionPreferences.getnMissedCleavages(enzyme.getName());
if (missedCleavages == null || enzymeMissedCleavages > missedCleavages) {
missedCleavages = enzymeMissedCleavages;
}
}
bw.write("max missed cleavages=" + missedCleavages);
bw.newLine();
}
bw.write("fasta file=\"" + searchParameters.getFastaFile().getAbsolutePath() + "\"");
bw.newLine();
bw.write("decoy mode=" + andromedaParameters.getDecoyMode());
bw.newLine();
bw.write("include contaminants=False");
bw.newLine();
if (andromedaParameters.isIncludeWater()) {
bw.write("include water=True");
} else {
bw.write("include water=False");
}
bw.newLine();
if (andromedaParameters.isIncludeAmmonia()) {
bw.write("include ammonia=True");
} else {
bw.write("include ammonia=False");
}
bw.newLine();
if (andromedaParameters.isDependentLosses()) {
bw.write("dependent losses=True");
} else {
bw.write("dependent losses=False");
}
bw.newLine();
bw.write("special aas=");
bw.newLine();
if (andromedaParameters.isFragmentAll()) {
bw.write("fragment all=True");
} else {
bw.write("fragment all=False");
}
bw.newLine();
if (andromedaParameters.isEmpiricalCorrection()) {
bw.write("empirical correction=True");
} else {
bw.write("empirical correction=False");
}
bw.newLine();
if (andromedaParameters.isHigherCharge()) {
bw.write("higher charges=True");
} else {
bw.write("higher charges=False");
}
bw.newLine();
bw.write("fragmentation type=" + andromedaParameters.getFragmentationMethod().name);
bw.newLine();
bw.write("max number of modifications=" + andromedaParameters.getMaxNumberOfModifications());
bw.newLine();
bw.write("min peptide length no enzyme=" + andromedaParameters.getMinPeptideLengthNoEnzyme());
bw.newLine();
bw.write("max peptide length no enzyme=" + andromedaParameters.getMaxPeptideLengthNoEnzyme());
bw.newLine();
if (andromedaParameters.isEqualIL()) {
bw.write("equal il=True");
} else {
bw.write("equal il=False");
}
bw.newLine();
bw.write("number of candidates=" + andromedaParameters.getNumberOfCandidates());
bw.newLine();
} finally {
bw.close();
}
return parameterFile;
}
/**
* Creates new form ProteinInferenceDialog.
*
* @param peptideShakerGUI
* @param inspectedMatch
* @param identification
*/
public ProteinInferenceDialog(
PeptideShakerGUI peptideShakerGUI, String inspectedMatch, Identification identification) {
super(peptideShakerGUI, true);
this.identification = identification;
this.peptideShakerGUI = peptideShakerGUI;
try {
this.inspectedMatch = identification.getProteinMatch(inspectedMatch);
previousMainMatch = this.inspectedMatch.getMainMatch();
} catch (Exception e) {
peptideShakerGUI.catchException(e);
this.dispose();
}
accessions = new ArrayList(Arrays.asList(ProteinMatch.getAccessions(inspectedMatch)));
for (String proteinAccession : accessions) {
if (identification.getProteinIdentification().contains(proteinAccession)) {
uniqueMatches.add(proteinAccession);
}
}
for (String proteinKey : identification.getProteinIdentification()) {
if (ProteinMatch.getNProteins(proteinKey) > 1
&& !associatedMatches.contains(proteinKey)
&& !proteinKey.equals(inspectedMatch)) {
for (String proteinAccession : accessions) {
if (proteinKey.contains(proteinAccession)) {
associatedMatches.add(proteinKey);
break;
}
}
}
}
initComponents();
// make sure that the scroll panes are see-through
proteinMatchJScrollPane.getViewport().setOpaque(false);
uniqueHitsJScrollPane.getViewport().setOpaque(false);
relatedHitsJScrollPane.getViewport().setOpaque(false);
groupClassJComboBox.setRenderer(new AlignedListCellRenderer(SwingConstants.CENTER));
PSParameter psParameter = new PSParameter();
try {
psParameter =
(PSParameter) identification.getProteinMatchParameter(inspectedMatch, psParameter);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
matchInfoLbl.setText(
"[Score: "
+ Util.roundDouble(psParameter.getProteinScore(), 2)
+ ", Confidence: "
+ Util.roundDouble(psParameter.getProteinConfidence(), 2)
+ "]");
// set up the table column properties
setColumnProperies();
// The index should be set in the design according to the PSParameter class static fields!
groupClassJComboBox.setSelectedIndex(psParameter.getGroupClass());
setLocationRelativeTo(peptideShakerGUI);
setVisible(true);
}
/**
* Returns the default reference for an identification.
*
* @param experimentReference the experiment reference
* @param sampleReference the sample reference
* @param replicateNumber the replicate number
* @return the default reference
*/
public static String getDefaultReference(
String experimentReference, String sampleReference, int replicateNumber) {
return Util.removeForbiddenCharacters(
experimentReference + "_" + sampleReference + "_" + replicateNumber + "_reporterQuant");
}
public void testDB()
throws SQLException, IOException, ClassNotFoundException, SQLException,
ClassNotFoundException, InterruptedException {
String path = this.getClass().getResource("IdentificationDBTest.class").getPath();
path = path.substring(1, path.indexOf("/target/"));
path += "/src/test/resources/experiment/testDB";
try {
ObjectsCache cache = new ObjectsCache();
cache.setAutomatedMemoryManagement(false);
cache.setCacheSize(0);
IdentificationDB idDB = new IdentificationDB(path, "testId", true, cache);
try {
String spectrumKey = "spectrum_file_cus_spectrum_title";
String peptideKey = "PEPTIDE";
String proteinKey = "test_protein";
SpectrumMatch testSpectrumMatch = new SpectrumMatch(spectrumKey);
ArrayList<String> testProteins = new ArrayList<String>();
testProteins.add("test protein1");
testProteins.add("test protein2");
Peptide peptide = new Peptide(peptideKey, new ArrayList<ModificationMatch>());
peptide.setParentProteins(testProteins);
testSpectrumMatch.addHit(
Advocate.mascot.getIndex(),
new PeptideAssumption(
peptide, 1, Advocate.mascot.getIndex(), new Charge(Charge.PLUS, 2), 0.1, "no file"),
false);
idDB.addSpectrumMatch(testSpectrumMatch);
peptide = new Peptide(peptideKey, new ArrayList<ModificationMatch>());
peptide.setParentProteins(testProteins);
PeptideMatch testPeptideMatch = new PeptideMatch(peptide, peptide.getKey());
idDB.addPeptideMatch(testPeptideMatch);
ProteinMatch testProteinMatch = new ProteinMatch(proteinKey);
idDB.addProteinMatch(testProteinMatch);
testSpectrumMatch = idDB.getSpectrumMatch(spectrumKey, true);
Assert.assertTrue(testSpectrumMatch.getKey().equals(spectrumKey));
HashMap<Integer, HashMap<Double, ArrayList<SpectrumIdentificationAssumption>>>
assumptionsMap = testSpectrumMatch.getAssumptionsMap();
HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> mascotAssumptions =
assumptionsMap.get(Advocate.mascot.getIndex());
Assert.assertTrue(mascotAssumptions.size() == 1);
ArrayList<Double> mascotScores = new ArrayList<Double>(mascotAssumptions.keySet());
Assert.assertTrue(mascotScores.size() == 1);
double bestScore = mascotScores.get(0);
Assert.assertTrue(bestScore == 0.1);
ArrayList<SpectrumIdentificationAssumption> bestAssumptions =
mascotAssumptions.get(bestScore);
PeptideAssumption bestAssumption = (PeptideAssumption) bestAssumptions.get(0);
Peptide bestPeptide = bestAssumption.getPeptide();
Assert.assertTrue(bestPeptide.getParentProteinsNoRemapping().size() == 2);
Assert.assertTrue(
bestPeptide.getParentProteinsNoRemapping().get(0).equals(testProteins.get(0)));
Assert.assertTrue(
bestPeptide.getParentProteinsNoRemapping().get(1).equals(testProteins.get(1)));
ArrayList<String> proteins = new ArrayList<String>();
proteins.add(proteinKey);
bestPeptide.setParentProteins(proteins);
idDB.updateMatch(testSpectrumMatch);
testSpectrumMatch = idDB.getSpectrumMatch(spectrumKey, true);
assumptionsMap = testSpectrumMatch.getAssumptionsMap();
mascotAssumptions = assumptionsMap.get(Advocate.mascot.getIndex());
Assert.assertTrue(mascotAssumptions.size() == 1);
mascotScores = new ArrayList<Double>(mascotAssumptions.keySet());
Assert.assertTrue(mascotScores.size() == 1);
bestScore = mascotScores.get(0);
Assert.assertTrue(bestScore == 0.1);
bestAssumptions = mascotAssumptions.get(bestScore);
bestAssumption = (PeptideAssumption) bestAssumptions.get(0);
bestPeptide = bestAssumption.getPeptide();
Assert.assertTrue(bestPeptide.getParentProteinsNoRemapping().size() == 1);
Assert.assertTrue(bestPeptide.getParentProteinsNoRemapping().get(0).equals(proteinKey));
testPeptideMatch = idDB.getPeptideMatch(peptideKey, true);
Assert.assertTrue(testPeptideMatch.getKey().equals(peptideKey));
testProteinMatch = idDB.getProteinMatch(proteinKey, true);
Assert.assertTrue(testProteinMatch.getKey().equals(proteinKey));
double testScore = 12.3;
PepnovoAssumptionDetails testParameter = new PepnovoAssumptionDetails();
testParameter.setRankScore(testScore);
idDB.addSpectrumMatchParameter(spectrumKey, testParameter);
testParameter =
(PepnovoAssumptionDetails)
idDB.getSpectrumMatchParameter(spectrumKey, testParameter, true);
Assert.assertTrue(testParameter.getRankScore() == testScore);
} finally {
idDB.close();
}
} finally {
File dbFolder = new File(path);
DerbyUtil.closeConnection();
Util.deleteDir(dbFolder);
}
}