/**
* Writes the desired section.
*
* @param identification the identification of the project
* @param identificationFeaturesGenerator the identification features generator of the project
* @param identificationParameters the identification parameters
* @param keys the keys of the protein matches to output
* @param nSurroundingAA the number of surrounding amino acids to export
* @param linePrefix the line prefix to use.
* @param validatedOnly whether only validated matches should be exported
* @param decoys whether decoy matches should be exported as well
* @param waitingHandler the waiting handler
* @throws IOException exception thrown whenever an error occurred while interacting with a file
* @throws SQLException thrown whenever an error occurred while interacting with the database
* @throws ClassNotFoundException thrown whenever an error occurred while deserializing a match
* from the database
* @throws InterruptedException thrown whenever a threading error occurred while interacting with
* the database
* @throws MzMLUnmarshallerException thrown whenever an error occurred while reading an mzML file
*/
public void writeSection(
Identification identification,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
ArrayList<String> keys,
int nSurroundingAA,
String linePrefix,
boolean validatedOnly,
boolean decoys,
WaitingHandler waitingHandler)
throws IOException, SQLException, ClassNotFoundException, InterruptedException,
MzMLUnmarshallerException {
if (waitingHandler != null) {
waitingHandler.setSecondaryProgressCounterIndeterminate(true);
}
if (header) {
writeHeader();
}
if (keys == null) {
keys = new ArrayList<String>(identification.getPeptideIdentification());
}
int line = 1;
if (waitingHandler != null) {
waitingHandler.setWaitingText("Exporting. Please Wait...");
waitingHandler.resetSecondaryProgressCounter();
waitingHandler.setMaxSecondaryProgressCounter(keys.size());
}
PSParameter psParameter = new PSParameter();
ArrayList<UrParameter> parameters = new ArrayList<UrParameter>(1);
parameters.add(psParameter);
PeptideMatchesIterator peptideMatchesIterator =
identification.getPeptideMatchesIterator(
keys, parameters, psmSection != null, parameters, waitingHandler);
while (peptideMatchesIterator.hasNext()) {
if (waitingHandler != null) {
if (waitingHandler.isRunCanceled()) {
return;
}
waitingHandler.increaseSecondaryProgressCounter();
}
PeptideMatch peptideMatch = peptideMatchesIterator.next();
String peptideKey = peptideMatch.getKey();
psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, psParameter);
if (!validatedOnly || psParameter.getMatchValidationLevel().isValidated()) {
if (decoys
|| !peptideMatch
.getTheoreticPeptide()
.isDecoy(identificationParameters.getSequenceMatchingPreferences())) {
boolean first = true;
if (indexes) {
if (linePrefix != null) {
writer.write(linePrefix);
}
writer.write(line + "");
first = false;
}
for (ExportFeature exportFeature : peptideFeatures) {
if (!first) {
writer.addSeparator();
} else {
first = false;
}
PsPeptideFeature peptideFeature = (PsPeptideFeature) exportFeature;
writer.write(
getfeature(
identification,
identificationFeaturesGenerator,
identificationParameters,
keys,
nSurroundingAA,
linePrefix,
peptideMatch,
psParameter,
peptideFeature,
validatedOnly,
decoys,
waitingHandler));
}
writer.newLine();
if (psmSection != null) {
String psmSectionPrefix = "";
if (linePrefix != null) {
psmSectionPrefix += linePrefix;
}
psmSectionPrefix += line + ".";
writer.increaseDepth();
if (waitingHandler != null) {
waitingHandler.setDisplayProgress(false);
}
psmSection.writeSection(
identification,
identificationFeaturesGenerator,
identificationParameters,
peptideMatch.getSpectrumMatchesKeys(),
psmSectionPrefix,
nSurroundingAA,
validatedOnly,
decoys,
waitingHandler);
if (waitingHandler != null) {
waitingHandler.setDisplayProgress(true);
}
writer.decreseDepth();
}
line++;
}
}
}
}
/**
* Returns the component of the section corresponding to the given feature.
*
* @param identification the identification of the project
* @param identificationFeaturesGenerator the identification features generator of the project
* @param identificationParameters the identification parameters
* @param keys the keys of the protein matches to output
* @param nSurroundingAA the number of surrounding amino acids to export
* @param linePrefix the line prefix to use.
* @param peptideMatch the peptide match
* @param psParameter the PeptideShaker parameters of the match
* @param peptideFeature the peptide feature to export
* @param validatedOnly whether only validated matches should be exported
* @param decoys whether decoy matches should be exported as well
* @param waitingHandler the waiting handler
* @return the component of the section corresponding to the given feature
* @throws IOException exception thrown whenever an error occurred while interacting with a file
* while mapping potential modification sites
* @throws InterruptedException exception thrown whenever a threading issue occurred while mapping
* potential modification sites
* @throws ClassNotFoundException exception thrown whenever an error occurred while deserializing
* an object from the ProteinTree
* @throws SQLException exception thrown whenever an error occurred while interacting with the
* ProteinTree
* @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException exception thrown whenever an error
* occurred while reading an mzML file
*/
public static String getfeature(
Identification identification,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
ArrayList<String> keys,
int nSurroundingAA,
String linePrefix,
PeptideMatch peptideMatch,
PSParameter psParameter,
PsPeptideFeature peptideFeature,
boolean validatedOnly,
boolean decoys,
WaitingHandler waitingHandler)
throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException,
InterruptedException, MzMLUnmarshallerException {
switch (peptideFeature) {
case accessions:
StringBuilder proteins = new StringBuilder();
ArrayList<String> accessions =
peptideMatch
.getTheoreticPeptide()
.getParentProteins(identificationParameters.getSequenceMatchingPreferences());
Collections.sort(accessions);
for (String accession : accessions) {
if (proteins.length() > 0) {
proteins.append("; ");
}
proteins.append(accession);
}
return proteins.toString();
case protein_description:
SequenceFactory sequenceFactory = SequenceFactory.getInstance();
StringBuilder descriptions = new StringBuilder();
accessions =
peptideMatch
.getTheoreticPeptide()
.getParentProteins(identificationParameters.getSequenceMatchingPreferences());
Collections.sort(accessions);
for (String accession : accessions) {
if (descriptions.length() > 0) {
descriptions.append("; ");
}
descriptions.append(sequenceFactory.getHeader(accession).getDescription());
}
return descriptions.toString();
case protein_groups:
HashSet<String> proteinGroups =
identification.getProteinMatches(peptideMatch.getTheoreticPeptide());
proteins = new StringBuilder();
ArrayList<String> proteinGroupsList = new ArrayList<String>(proteinGroups);
Collections.sort(proteinGroupsList);
if (proteinGroupsList.size() > 1) {
identification.loadProteinMatchParameters(
proteinGroupsList, psParameter, waitingHandler, false);
}
psParameter = new PSParameter();
for (String proteinGroup : proteinGroupsList) {
if (identification.getProteinIdentification().contains(proteinGroup)) {
psParameter =
(PSParameter) identification.getProteinMatchParameter(proteinGroup, psParameter);
if (proteins.length() > 0) {
proteins.append("; ");
}
List<String> groupAccessions = Arrays.asList(ProteinMatch.getAccessions(proteinGroup));
Collections.sort(groupAccessions);
boolean first = true;
for (String accession : groupAccessions) {
if (first) {
first = false;
} else {
proteins.append(", ");
}
proteins.append(accession);
}
proteins.append(" (");
proteins.append(psParameter.getMatchValidationLevel().getName());
proteins.append(")");
}
}
return proteins.toString();
case best_protein_group_validation:
MatchValidationLevel bestProteinValidationLevel = MatchValidationLevel.none;
proteinGroups = identification.getProteinMatches(peptideMatch.getTheoreticPeptide());
proteinGroupsList = new ArrayList<String>(proteinGroups);
Collections.sort(proteinGroupsList);
if (proteinGroupsList.size() > 1) {
identification.loadProteinMatchParameters(
proteinGroupsList, psParameter, waitingHandler, false);
}
psParameter = new PSParameter();
for (String proteinGroup : proteinGroupsList) {
if (identification.getProteinIdentification().contains(proteinGroup)) {
psParameter =
(PSParameter) identification.getProteinMatchParameter(proteinGroup, psParameter);
if (psParameter.getMatchValidationLevel().getIndex()
> bestProteinValidationLevel.getIndex()) {
bestProteinValidationLevel = psParameter.getMatchValidationLevel();
}
}
}
return bestProteinValidationLevel.getName();
case confidence:
return psParameter.getPeptideConfidence() + "";
case decoy:
if (peptideMatch
.getTheoreticPeptide()
.isDecoy(identificationParameters.getSequenceMatchingPreferences())) {
return "1";
} else {
return "0";
}
case hidden:
if (psParameter.isHidden()) {
return "1";
} else {
return "0";
}
case localization_confidence:
return getPeptideModificationLocations(
peptideMatch, identificationParameters.getSearchParameters().getPtmSettings())
+ "";
case pi:
return psParameter.getProteinInferenceClassAsString();
case position:
accessions =
peptideMatch
.getTheoreticPeptide()
.getParentProteins(identificationParameters.getSequenceMatchingPreferences());
Collections.sort(accessions);
Peptide peptide = peptideMatch.getTheoreticPeptide();
String start = "";
for (String proteinAccession : accessions) {
if (!start.equals("")) {
start += "; ";
}
Protein protein = SequenceFactory.getInstance().getProtein(proteinAccession);
ArrayList<Integer> starts =
protein.getPeptideStart(
peptide.getSequence(), identificationParameters.getSequenceMatchingPreferences());
Collections.sort(starts);
boolean first = true;
for (int startAa : starts) {
if (first) {
first = false;
} else {
start += ", ";
}
start += startAa;
}
}
return start;
case psms:
return peptideMatch.getSpectrumCount() + "";
case variable_ptms:
return Peptide.getPeptideModificationsAsString(peptideMatch.getTheoreticPeptide(), true);
case fixed_ptms:
return Peptide.getPeptideModificationsAsString(peptideMatch.getTheoreticPeptide(), false);
case score:
return psParameter.getPeptideScore() + "";
case raw_score:
return psParameter.getPeptideProbabilityScore() + "";
case sequence:
return peptideMatch.getTheoreticPeptide().getSequence();
case missed_cleavages:
peptide = peptideMatch.getTheoreticPeptide();
Integer nMissedCleavages =
peptide.getNMissedCleavages(
identificationParameters.getSearchParameters().getDigestionPreferences());
if (nMissedCleavages == null) {
nMissedCleavages = 0;
}
return nMissedCleavages + "";
case modified_sequence:
return peptideMatch
.getTheoreticPeptide()
.getTaggedModifiedSequence(
identificationParameters.getSearchParameters().getPtmSettings(),
false,
false,
true);
case starred:
if (psParameter.isStarred()) {
return "1";
} else {
return "0";
}
case aaBefore:
peptide = peptideMatch.getTheoreticPeptide();
accessions =
peptide.getParentProteins(identificationParameters.getSequenceMatchingPreferences());
Collections.sort(accessions);
String subSequence = "";
for (String proteinAccession : accessions) {
if (!subSequence.equals("")) {
subSequence += "; ";
}
HashMap<Integer, String[]> surroundingAAs =
SequenceFactory.getInstance()
.getProtein(proteinAccession)
.getSurroundingAA(
peptide.getSequence(),
nSurroundingAA,
identificationParameters.getSequenceMatchingPreferences());
ArrayList<Integer> starts = new ArrayList<Integer>(surroundingAAs.keySet());
Collections.sort(starts);
boolean first = true;
for (int startAa : starts) {
if (first) {
first = false;
} else {
subSequence += ", ";
}
subSequence += surroundingAAs.get(startAa)[0];
}
}
return subSequence;
case aaAfter:
peptide = peptideMatch.getTheoreticPeptide();
accessions =
peptide.getParentProteins(identificationParameters.getSequenceMatchingPreferences());
Collections.sort(accessions);
subSequence = "";
for (String proteinAccession : accessions) {
if (!subSequence.equals("")) {
subSequence += "; ";
}
HashMap<Integer, String[]> surroundingAAs =
SequenceFactory.getInstance()
.getProtein(proteinAccession)
.getSurroundingAA(
peptide.getSequence(),
nSurroundingAA,
identificationParameters.getSequenceMatchingPreferences());
ArrayList<Integer> starts = new ArrayList<Integer>(surroundingAAs.keySet());
Collections.sort(starts);
boolean first = true;
for (int startAa : starts) {
if (first) {
first = false;
} else {
subSequence += ", ";
}
subSequence += surroundingAAs.get(startAa)[1];
}
}
return subSequence;
case nValidatedProteinGroups:
peptide = peptideMatch.getTheoreticPeptide();
return identificationFeaturesGenerator.getNValidatedProteinGroups(peptide, waitingHandler)
+ "";
case unique_database:
peptide = peptideMatch.getTheoreticPeptide();
if (identification.isUniqueInDatabase(peptide)) {
return "1";
} else {
return "0";
}
case validated:
return psParameter.getMatchValidationLevel().toString();
case validated_psms:
return identificationFeaturesGenerator.getNValidatedSpectraForPeptide(peptideMatch.getKey())
+ "";
case probabilistic_score:
PSPtmScores ptmScores = new PSPtmScores();
ptmScores = (PSPtmScores) peptideMatch.getUrParam(ptmScores);
if (ptmScores != null) {
StringBuilder result = new StringBuilder();
ArrayList<String> modList = new ArrayList<String>(ptmScores.getScoredPTMs());
Collections.sort(modList);
for (String mod : modList) {
PtmScoring ptmScoring = ptmScores.getPtmScoring(mod);
ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getProbabilisticSites());
if (!sites.isEmpty()) {
Collections.sort(sites);
if (result.length() > 0) {
result.append(", ");
}
result.append(mod).append(" (");
boolean firstSite = true;
for (int site : sites) {
if (firstSite) {
firstSite = false;
} else {
result.append(", ");
}
result.append(site).append(": ").append(ptmScoring.getProbabilisticScore(site));
}
result.append(")");
}
}
return result.toString();
}
return "";
case d_score:
StringBuilder result = new StringBuilder();
ptmScores = new PSPtmScores();
ptmScores = (PSPtmScores) peptideMatch.getUrParam(ptmScores);
if (ptmScores != null) {
ArrayList<String> modList = new ArrayList<String>(ptmScores.getScoredPTMs());
Collections.sort(modList);
for (String mod : modList) {
PtmScoring ptmScoring = ptmScores.getPtmScoring(mod);
ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getDSites());
if (!sites.isEmpty()) {
Collections.sort(sites);
if (result.length() > 0) {
result.append(", ");
}
result.append(mod).append(" (");
boolean firstSite = true;
for (int site : sites) {
if (firstSite) {
firstSite = false;
} else {
result.append(", ");
}
result.append(site).append(": ").append(ptmScoring.getDeltaScore(site));
}
result.append(")");
}
}
return result.toString();
}
return "";
case confident_modification_sites:
String sequence = peptideMatch.getTheoreticPeptide().getSequence();
return identificationFeaturesGenerator.getConfidentPtmSites(peptideMatch, sequence);
case confident_modification_sites_number:
return identificationFeaturesGenerator.getConfidentPtmSitesNumber(peptideMatch);
case ambiguous_modification_sites:
sequence = peptideMatch.getTheoreticPeptide().getSequence();
return identificationFeaturesGenerator.getAmbiguousPtmSites(peptideMatch, sequence);
case ambiguous_modification_sites_number:
return identificationFeaturesGenerator.getAmbiguousPtmSiteNumber(peptideMatch);
case confident_phosphosites:
ArrayList<String> modifications = new ArrayList<String>();
for (String ptm :
identificationParameters
.getSearchParameters()
.getPtmSettings()
.getAllNotFixedModifications()) {
if (ptm.contains("Phospho")) {
modifications.add(ptm);
}
}
return identificationFeaturesGenerator.getConfidentPtmSites(
peptideMatch, peptideMatch.getTheoreticPeptide().getSequence(), modifications);
case confident_phosphosites_number:
modifications = new ArrayList<String>();
for (String ptm :
identificationParameters
.getSearchParameters()
.getPtmSettings()
.getAllNotFixedModifications()) {
if (ptm.contains("Phospho")) {
modifications.add(ptm);
}
}
return identificationFeaturesGenerator.getConfidentPtmSitesNumber(
peptideMatch, modifications);
case ambiguous_phosphosites:
modifications = new ArrayList<String>();
for (String ptm :
identificationParameters
.getSearchParameters()
.getPtmSettings()
.getAllNotFixedModifications()) {
if (ptm.contains("Phospho")) {
modifications.add(ptm);
}
}
return identificationFeaturesGenerator.getAmbiguousPtmSites(
peptideMatch, peptideMatch.getTheoreticPeptide().getSequence(), modifications);
case ambiguous_phosphosites_number:
modifications = new ArrayList<String>();
for (String ptm :
identificationParameters
.getSearchParameters()
.getPtmSettings()
.getAllNotFixedModifications()) {
if (ptm.contains("Phospho")) {
modifications.add(ptm);
}
}
return identificationFeaturesGenerator.getAmbiguousPtmSiteNumber(
peptideMatch, modifications);
default:
return "Not implemented";
}
}
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);
}
}