Remove code for ignoring ambiguous spectra from MSFReader.cpp

pwiz_tools/BiblioSpec/src/MSFReader.cpp

@@ -310,37 +310,6 @@ namespace BiblioSpec
 
  void MSFReader::collectPsms() {
  sqlite3_stmt* statement;
- map<int, double> alts; // peptide id --> alt score, for breaking ties when q-values are identical
- vector<string> altScoreNames;
- altScoreNames.push_back("XCorr");
- altScoreNames.push_back("IonScore");
-
- if (tableExists(msfFile_, "TargetPsms")) {
- for (vector<string>::const_iterator i = altScoreNames.begin(); i != altScoreNames.end(); ++i) {
- if (!columnExists(msfFile_, "TargetPsms", *i)) {
- continue;
- }
- statement = getStmt("SELECT PeptideID, " + *i + " FROM TargetPsms");
- while (hasNext(&statement)) {
- alts[sqlite3_column_int(statement, 0)] = sqlite3_column_double(statement, 1);
- }
- break;
- }
- } else if (tableExists(msfFile_, "PeptideScores") && tableExists(msfFile_, "ProcessingNodeScores")) {
- for (vector<string>::const_iterator i = altScoreNames.begin(); i != altScoreNames.end(); ++i) {
- statement = getStmt(
- "SELECT PeptideID, ScoreValue "
- "FROM PeptideScores JOIN ProcessingNodeScores ON PeptideScores.ScoreID = ProcessingNodeScores.ScoreID "
- "WHERE ScoreName = '" + *i + "'");
- while (hasNext(&statement)) {
- alts[sqlite3_column_int(statement, 0)] = sqlite3_column_double(statement, 1);
- }
- if (!alts.empty()) {
- break;
- }
- }
- }
-
  int resultCount, pepConfidence, protConfidence;
  PSM_SCORE_TYPE scoreType;
  getScoreInfo(&statement, &resultCount, &scoreType, &pepConfidence, &protConfidence);
@@ -349,7 +318,6 @@ namespace BiblioSpec
  ProgressIndicator progress(resultCount);
 
  initFileNameMap();
- map<string, ProcessedMsfSpectrum> processedSpectra;
  ModSet modSet = ModSet(msfFile_, !versionLess(2, 2) || filtered_);
  map<int, int> fileIdMap = getFileIds();
 
@@ -390,56 +358,7 @@ namespace BiblioSpec
  continue;
  }
 
- auto altIter = alts.find(peptideId); 
- double altScore = (altIter != alts.end()) ? altIter->second : -std::numeric_limits<double>::max();
-
- // check if we already processed a peptide that references this spectrum
- auto processedSpectraSearch = processedSpectra.find(specId);
- if (processedSpectraSearch != processedSpectra.end()) {
- ProcessedMsfSpectrum& processed = processedSpectraSearch->second;
- // not an ambigous spectrum (yet)
- if (!processed.ambiguous) {
- if (qvalue > processed.qvalue || (qvalue == processed.qvalue && altScore < processed.altScore)) { // worse than other score, skip this
- Verbosity::debug("Peptide %d (%s) had a worse score than another peptide (%s) "
- "referencing spectrum %d (ignoring this peptide).",
- peptideId, sequence.c_str(), processed.psm->unmodSeq.c_str(), specId.c_str());
- continue;
- } else if (qvalue == processed.qvalue && altScore == processed.altScore) { // equal, discard other and skip this
- Verbosity::debug("Peptide %d (%s) had the same score as another peptide (%s) "
- "referencing spectrum %d (ignoring both peptides).",
- peptideId, sequence.c_str(), processed.psm->unmodSeq.c_str(), specId.c_str());
-
- removeFromFileMap(processed.psm);
- delete processed.psm;
-
- processed.psm = NULL;
- processed.ambiguous = true;
- continue;
- } else { // better than other score, discard other
- Verbosity::debug("Peptide %d (%s) had a better score than another peptide (%s) "
- "referencing spectrum %d (ignoring other peptide).",
- peptideId, sequence.c_str(), processed.psm->unmodSeq.c_str(), specId.c_str());
- removeFromFileMap(processed.psm);
- curPSM_ = processed.psm;
- curPSM_->mods.clear();
- processed.qvalue = qvalue;
- processed.altScore = altScore;
- }
- } else { // ambigous spectrum, check if score is better
- Verbosity::debug("Peptide %d (%s) with score %f references same spectrum as other peptides "
- "that had score %f.", peptideId, sequence.c_str(), qvalue, processed.qvalue);
- if (qvalue < processed.qvalue || (qvalue == processed.qvalue && altScore > processed.altScore)) {
- curPSM_ = new PSM();
- processedSpectraSearch->second = ProcessedMsfSpectrum(curPSM_, qvalue, altScore);
- } else {
- continue;
- }
- }
- } else {
- // unseen spectrum
- curPSM_ = new PSM();
- processedSpectra[specId] = ProcessedMsfSpectrum(curPSM_, qvalue, altScore);
- }
+ curPSM_ = new PSM();
 
  if (findItr->second->charge > 0)
  curPSM_->charge = findItr->second->charge;

pwiz_tools/BiblioSpec/tests/Jamfile.jam

@@ -269,6 +269,7 @@ blib-test-build tinyPlink-proxl : -o : output/tinyPlink-proxl.blib : tinyPlink-p
 blib-test-build tinyPeptideProphet-proxl : -o : output/tinyPeptideProphet-proxl.blib : tinyPeptideProphet-proxl.check zbuild.skip-lines : $(TEST_INPUTS_PATH)/tinyPeptideProphet.proxl.xml ;
 blib-test-build tinyMerox-proxl : -o : output/tinyMerox-proxl.blib : tinyMerox-proxl.check zbuild.skip-lines : $(TEST_INPUTS_PATH)/tinyMerox.proxl.xml ;
 blib-test-build tiny-msf : --unicode -o : output/tiny-msf.blib : tiny-msf.check zbuild.skip-lines : $(TEST_INPUTS_PATH)/tiny.msf ;
+blib-test-build tiny-msf-keep : --unicode -o -K : output/tiny-msf-keep.blib : tiny-msf-keep.check zbuild.skip-lines : $(TEST_INPUTS_PATH)/tiny.msf ;
 blib-test-build tiny-v2-msf : -o : output/tiny-v2-msf.blib : tiny-v2-msf.check zbuild.skip-lines : $(TEST_INPUTS_PATH)/tiny-v2.msf ;
 blib-test-build tiny-v2-filtered-pdResult : -o : output/tiny-v2-filtered-pdResult.blib : tiny-v2-filtered-pdResult.check zbuild.skip-lines : $(TEST_INPUTS_PATH)/tiny-v2-filtered.pdResult ;
 blib-test-build md_special_filtered-pdResult : --unicode -o : output/md_special_filtered-pdResult.blib : md_special_filtered-pdResult.check zbuild.skip-lines : $(TEST_INPUTS_PATH)/md_special_filtered.pdResult ;

pwiz_tools/BiblioSpec/tests/reference/tiny-msf-keep.check

@@ -0,0 +1,50 @@
+libLSID numSpecs majorVersion minorVersion
+urn:lsid:proteome.gs.washington.edu:spectral_library:bibliospec:redundant:tiny-msf-keep.blib 6 1 10
+id RefSpectraID position mass
+1 1 1 4.008491
+2 1 2 4.008491
+3 1 7 4.008491
+4 2 3 4.008491
+5 2 4 4.008491
+6 2 7 4.008491
+7 3 1 4.008491
+8 3 2 4.008491
+9 3 7 4.008491
+10 4 1 4.008491
+11 4 3 4.008491
+12 4 7 4.008491
+13 5 1 15.994915
+14 5 8 15.994915
+15 5 10 4.008491
+id peptideSeq precursorMZ precursorCharge peptideModSeq prevAA nextAA copies numPeaks ionMobility collisionalCrossSectionSqA ionMobilityHighEnergyOffset ionMobilityType retentionTime startTime endTime totalIonCurrent moleculeName chemicalFormula precursorAdduct inchiKey otherKeys fileID SpecIDinFile score scoreType
+1 KKLVPLK 419.81906737 2 K[+4.0]K[+4.0]LVPLK[+4.0] - - 1 90 0.0 0.0 0.0 0 0.32088 N/A N/A 3448.02592301 N/A N/A N/A N/A N/A 1 2 0.002 1
+2 VPKKILK 419.81915892 2 VPK[+4.0]K[+4.0]ILK[+4.0] - - 1 95 0.0 0.0 0.0 0 1.12651166 N/A N/A 4332.04377079 N/A N/A N/A N/A N/A 1 4 0.006 1
+3 KKLVPLK 419.81915892 2 K[+4.0]K[+4.0]LVPLK[+4.0] - - 1 95 0.0 0.0 0.0 0 1.12651166 N/A N/A 4332.04377079 N/A N/A N/A N/A N/A 1 4 0.009 1
+4 KLKVIPK 419.81921996 2 K[+4.0]LK[+4.0]VIPK[+4.0] - - 1 100 0.0 0.0 0.0 0 2.24853 N/A N/A 4803.68319678 N/A N/A N/A N/A N/A 1 6 0.002 1
+5 MASASGAMAK 481.22015990 2 M[+16.0]ASASGAM[+16.0]AK[+4.0] - - 1 120 0.0 0.0 0.0 0 2.85028666 N/A N/A 7404.39071369 N/A N/A N/A N/A N/A 1 9 0.01 1
+6 RPVTPKK 413.76981200 2 RPVTPKK - - 1 175 0.0 0.0 0.0 0 2.87913166 N/A N/A 16087.57 N/A N/A N/A N/A N/A 2 10 0.002 1
+id fileName idFileName cutoffScore
+1 D:/Elite_MAM/MITO_03.raw /BiblioSpec/tests/inputs/试验_tiny.msf -1.0
+2 X:/Test.raw /BiblioSpec/tests/inputs/试验_tiny.msf -1.0
+id scoreType probabilityType
+0 UNKNOWN NOT_A_PROBABILITY_VALUE
+1 PERCOLATOR QVALUE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+2 PEPTIDE PROPHET SOMETHING PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT
+3 SPECTRUM MILL NOT_A_PROBABILITY_VALUE
+4 IDPICKER FDR PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+5 MASCOT IONS SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+6 TANDEM EXPECTATION VALUE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+7 PROTEIN PILOT CONFIDENCE PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT
+8 SCAFFOLD SOMETHING PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT
+9 WATERS MSE PEPTIDE SCORE NOT_A_PROBABILITY_VALUE
+10 OMSSA EXPECTATION SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+11 PROTEIN PROSPECTOR EXPECTATION SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+12 SEQUEST XCORR PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+13 MAXQUANT SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+14 MORPHEUS SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+15 MSGF+ SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+16 PEAKS CONFIDENCE SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+17 BYONIC SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+18 PEPTIDE SHAKER CONFIDENCE PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT
+19 GENERIC Q-VALUE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+20 HARDKLOR IDOTP PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT

pwiz_tools/BiblioSpec/tests/reference/tiny-msf.check

@@ -1,24 +1,20 @@
 libLSID numSpecs majorVersion minorVersion
-urn:lsid:proteome.gs.washington.edu:spectral_library:bibliospec:redundant:tiny-msf.blib 5 1 10
+urn:lsid:proteome.gs.washington.edu:spectral_library:bibliospec:redundant:tiny-msf.blib 4 1 10
 id RefSpectraID position mass
 1 1 1 4.008491
 2 1 2 4.008491
 3 1 7 4.008491
-4 2 3 4.008491
-5 2 4 4.008491
+4 2 1 4.008491
+5 2 3 4.008491
 6 2 7 4.008491
-7 3 1 4.008491
-8 3 3 4.008491
-9 3 7 4.008491
-10 4 1 15.994915
-11 4 8 15.994915
-12 4 10 4.008491
+7 3 1 15.994915
+8 3 8 15.994915
+9 3 10 4.008491
 id peptideSeq precursorMZ precursorCharge peptideModSeq prevAA nextAA copies numPeaks ionMobility collisionalCrossSectionSqA ionMobilityHighEnergyOffset ionMobilityType retentionTime startTime endTime totalIonCurrent moleculeName chemicalFormula precursorAdduct inchiKey otherKeys fileID SpecIDinFile score scoreType
 1 KKLVPLK 419.81906737 2 K[+4.0]K[+4.0]LVPLK[+4.0] - - 1 90 0.0 0.0 0.0 0 0.32088 N/A N/A 3448.02592301 N/A N/A N/A N/A N/A 1 2 0.002 1
-2 VPKKILK 419.81915892 2 VPK[+4.0]K[+4.0]ILK[+4.0] - - 1 95 0.0 0.0 0.0 0 1.12651166 N/A N/A 4332.04377079 N/A N/A N/A N/A N/A 1 4 0.006 1
-3 KLKVIPK 419.81921996 2 K[+4.0]LK[+4.0]VIPK[+4.0] - - 1 100 0.0 0.0 0.0 0 2.24853 N/A N/A 4803.68319678 N/A N/A N/A N/A N/A 1 6 0.002 1
-4 MASASGAMAK 481.22015990 2 M[+16.0]ASASGAM[+16.0]AK[+4.0] - - 1 120 0.0 0.0 0.0 0 2.85028666 N/A N/A 7404.39071369 N/A N/A N/A N/A N/A 1 9 0.01 1
-5 RPVTPKK 413.76981200 2 RPVTPKK - - 1 175 0.0 0.0 0.0 0 2.87913166 N/A N/A 16087.57 N/A N/A N/A N/A N/A 2 10 0.002 1
+2 KLKVIPK 419.81921996 2 K[+4.0]LK[+4.0]VIPK[+4.0] - - 1 100 0.0 0.0 0.0 0 2.24853 N/A N/A 4803.68319678 N/A N/A N/A N/A N/A 1 6 0.002 1
+3 MASASGAMAK 481.22015990 2 M[+16.0]ASASGAM[+16.0]AK[+4.0] - - 1 120 0.0 0.0 0.0 0 2.85028666 N/A N/A 7404.39071369 N/A N/A N/A N/A N/A 1 9 0.01 1
+4 RPVTPKK 413.76981200 2 RPVTPKK - - 1 175 0.0 0.0 0.0 0 2.87913166 N/A N/A 16087.57 N/A N/A N/A N/A N/A 2 10 0.002 1
 id fileName idFileName cutoffScore
 1 D:/Elite_MAM/MITO_03.raw /BiblioSpec/tests/inputs/试验_tiny.msf -1.0
 2 X:/Test.raw /BiblioSpec/tests/inputs/试验_tiny.msf -1.0
@@ -43,3 +39,4 @@ id scoreType probabilityType
 17 BYONIC SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
 18 PEPTIDE SHAKER CONFIDENCE PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT
 19 GENERIC Q-VALUE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT
+20 HARDKLOR IDOTP PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT

pwiz_tools/Skyline/TestPerf/PerfThermoFAIMSTest.cs

@@ -120,7 +120,7 @@ private void TestPopulateDocumentFromLibrary()
  // Add all peptides
  var filterMatchedPeptidesDlg = ShowDialog<FilterMatchedPeptidesDlg>(viewLibUI.AddAllPeptides);
  var docBefore = WaitForProteinMetadataBackgroundLoaderCompletedUI();
- using (new CheckDocumentState(1, 8433, 10882, 43484))
+ using (new CheckDocumentState(1, 8591, 11057, 44174))
  {
  RunDlg<MultiButtonMsgDlg>(filterMatchedPeptidesDlg.OkDialog, addLibraryPepsDlg =>
  {
@@ -146,6 +146,7 @@ private void TestWizardBuildDocumentLibraryAndFinish(string documentFile)
  RunUI(() =>
  {
  Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page);
+ importPeptideSearchDlg.BuildPepSearchLibControl.IncludeAmbiguousMatches = true;
  importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(SearchFiles);
  });
  WaitForConditionUI(() => importPeptideSearchDlg.IsEarlyFinishButtonEnabled);