C++ (Cpp) Spectrum::getScanNumberの例

コード例 #1

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ファイル: MSSingleScan.cpp プロジェクト: AndSi/percolator

//#ifdef _MSC_VER 
//#ifndef MSSINGLESCAN_MAIN
//int mssinglescan_main(int argc, char * argv[] ) {
//#else
//int main(int argc, char *argv[]){
//#endif
//#else
int main(int argc, char *argv[]){
//#endif


	//Here are all the variable we are going to need
	MSReader r;
	Spectrum s;
  int j;

  if(argc==1){
    printf("DESCRIPTION: Reads an MS/MS spectrum from any MSToolkit supported file type and outputs to screen in MS2 format.\n\n");
    printf("USAGE: MSSingleScan [scan number] [file]\n");
    exit(0);
  };

	r.readFile(argv[2],s,atoi(argv[1]));
  if(s.getScanNumber()==0) exit(-1);
  printf("S\t%d\t%d\t%.*f\n",s.getScanNumber(),s.getScanNumber(),2,s.getMZ());
	if(s.getRTime()>0) printf("I\tRTime\t%.*f\n",4,s.getRTime());
	for(j=0;j<s.sizeZ();j++){
		printf("Z\t%d\t%.*f\n",s.atZ(j).z,2,s.atZ(j).mz);
	};

	for(j=0;j<s.size();j++){
		printf("%.4f %.4f\n",s.at(j).mz,s.at(j).intensity);
	};

  return 0;

};

コード例 #2

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ファイル: SearchLibrary.cpp プロジェクト: wolski/bibliospec2.0

// assumes at least one spectrum in allRefs
void SearchLibrary::runSearch(Spectrum& s)
{
    scoreMatches(s, cachedSpectra_, targetMatches_);
    scoreMatches(s, cachedDecoySpectra_, decoyMatches_);

    // keep scores from all target psms for estimating Weibull parameters
    vector<double> allScores;
    if(compute_pvalues_){
        for(size_t i=0; i < targetMatches_.size(); i++){
            double dotp = targetMatches_[i].getScore(DOTP);
            allScores.push_back(dotp);
        }
    }

    // there may have been spectra in cachedSpectra_ but none at the
    // correct charge state.  Check again
    if( targetMatches_.size() == 0 ){
        Verbosity::warn("No library spectra found for query %d "
                        "(precursor m/z %.2f).", s.getScanNumber(), s.getMz());
        return;
    }
    if( compute_pvalues_ ){
        addNullScores(s, allScores);
    }

    // sort the matches descending
    sort(targetMatches_.begin(), targetMatches_.end(), compMatchDotScore); 
    sort(decoyMatches_.begin(), decoyMatches_.end(), compMatchDotScore); 

    setRank();
    
    if( printAll_ ){
        cout << "spec " << s.getScanNumber() << endl;
    }

    if( compute_pvalues_ ){
        weibullEstimator_.estimateParams(allScores);
        
        // print params to file
        if( weibullParamFile_.is_open() ){
            weibullParamFile_ << s.getScanNumber() << "\t"
                              << weibullEstimator_.getEta() << "\t"
                              << weibullEstimator_.getBeta() << "\t"
                              << weibullEstimator_.getShift() << "\t"
                              << weibullEstimator_.getCorrelation() << "\t"
                              << weibullEstimator_.getNumPointsFit() 
                //(int)(allScores.size() * fraction_to_fit_)
                              << endl;
        }
        setMatchesPvalues(allScores.size());
    }
}

コード例 #3

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ファイル: SearchLibrary.cpp プロジェクト: wolski/bibliospec2.0

/**
 *  Generate more scores by creating decoy spectra and comparing them
 *  to query.  Create one decoy for each target until there are the
 *  minimum number of scores.  Do not save decoy spectrum or its
 *  Match.  Makes no changes to cachedSpectra_.
 */
void SearchLibrary::addNullScores(Spectrum s, vector<double>& allScores){
    int shiftAmount = 5;

    while((int)allScores.size() < minWeibullScores_) {
        int specAdded = 0; // make sure spectra were successfully added
        
        //loop through all candidate refs, create shifted spectrum, compare
        for(size_t i=0; i < targetMatches_.size(); i++) {
            const RefSpectrum* targetSpec = targetMatches_.at(i).getRefSpec();
            RefSpectrum* decoySpec = targetSpec->newDecoy(shiftAmount,
                                                          shiftRawSpectra_);
            if( decoySpec == NULL ){
                continue;
            }
            specAdded++;
            Match thisMatch(&s, decoySpec); // spectrum deleted with match?
            thisMatch.setMatchLibID(0);
            Verbosity::comment(V_ALL, 
                      "Comparing query spec %d and shifted library spec %d",
                      s.getScanNumber(), decoySpec->getLibSpecID() );
            
            DotProduct::compare(thisMatch);
            allScores.push_back(thisMatch.getScore(DOTP));
            
        } // next ref spectrum

        shiftAmount += 5;

        if( specAdded == 0 ){
            break;  // avoid infinite loop if number of scores not increasing
        }
    } // next pass through all ref spectra
}

コード例 #4

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ファイルを表示

ファイル: SearchLibrary.cpp プロジェクト: wolski/bibliospec2.0

/**
 * Compare the given query spectrum to all library spectra.  Create a
 * match for each and add to matches.
 */
void SearchLibrary::scoreMatches(Spectrum& s, deque<RefSpectrum*>& spectra,
                                 vector<Match>& matches ){
    Verbosity::debug("Scoring %d matches.", spectra.size());
    // get the charge states we will search
    const vector<int>& charges = s.getPossibleCharges();
    
    // compare all ref spec to query, create match for each
    for(size_t i=0; i< spectra.size(); i++) {
        // is there a better place to check this?
        if(spectra.at(i)->getNumProcessedPeaks() == 0 ){ 
            Verbosity::debug("Skipping library spectrum %d.  No peaks.", 
                             spectra.at(i)->getLibSpecID());
            continue;
        }
        
        if( ! checkCharge(charges, spectra.at(i)->getCharge()) ){
            continue;
        }
        
        Match thisMatch(&s, spectra.at(i));  
        
        thisMatch.setMatchLibID(spectra.at(i)->getLibID());
        
        Verbosity::comment(V_ALL, "Comparing query spec %d and library spec %d",
                           s.getScanNumber(), spectra.at(i)->getLibSpecID());
        
        DotProduct::compare(thisMatch); //static method
        
        // save match for reporting
        matches.push_back(thisMatch);
    }  
}

コード例 #5

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ファイル: CPeptideDatabase.cpp プロジェクト: mhoopmann/silactor

bool CPeptideDatabase::readMascot(char* mascotFile, char* dataFile){
  MSReader r;
  MascotParser p;
  Spectrum s;
  MascotLite m;

  int i;
  int percent=0;

  p.clear();
  p.readText(mascotFile);

  if(p.isDistiller()){
    cout << mascotFile << "\t" << p.size() << " peptides from Distiller, no need for RT lookup." << endl;
  } else if(p.hasRTime()){
    cout << mascotFile << "\t" << p.size() << " peptides have RT already, no need for lookup." << endl;
  } else {
    cout << mascotFile << "\tLooking up retention times for " << p.size() << " Mascot peptides..." << endl;
    cout << percent;
    r.readFile(dataFile,s);
  }

  for(i=0;i<p.size();i++){
    if(p.isDistiller()||p.hasRTime()){ 
      m.rTime=p[i].rTime;
    } else {
      if( (int)i*100/p.size() > percent){
        percent=(int)i*100/p.size();
        cout << "\b\b\b" << percent;
      }

      r.readFile(NULL,s,p[i].scanNum);
      if(s.getScanNumber()==0){
        cout << "Scan not found. Please check that correct data file is used. Stopping Mascot parsing." << endl;
        return false;
      }
      m.rTime=s.getRTime();
    }
    m.charge=p[i].charge;
    m.fileID=fileID;
    m.monoMass=p[i].zeroMass;
    m.scanNum=p[i].scanNum;
    strcpy(m.peptide,p[i].sequence_Long);
    strcpy(m.protein,p[i].gene);
    mascot.push_back(m);
  }
  cout << "  Done!" << endl;

  fileID++;

  return true;
}

コード例 #6

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