PeptideMatcherTest.cpp File Reference

#include "PeptideMatcher.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Functions
PidfPtr	makePeptideID_dataFetcher (const char *samplePepXML)
SpectrumQuery	makeSpectrumQuery (double precursorNeutralMass, double rt, int charge, string sequence, double score, int startScan, int endScan)
FeaturePtr	makeFeature (double mz, double retentionTime)
void	test ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0
const char *	samplePepXML_a = "</msms_pipeline_analysis>\n"
const char *	samplePepXML_b = "</msms_pipeline_analysis>\n"

---

Function Documentation

PidfPtr makePeptideID_dataFetcher

(

const char *

samplePepXML

)

Definition at line 120 of file PeptideMatcherTest.cpp.

{
    istringstream iss(samplePepXML);
    PidfPtr pidf(new PeptideID_dataFetcher(iss));

    return pidf;

}

SpectrumQuery makeSpectrumQuery	(	double	precursorNeutralMass,
		double	rt,
		int	charge,
		string	sequence,
		double	score,
		int	startScan,
		int	endScan
	)

Definition at line 129 of file PeptideMatcherTest.cpp.

References pwiz::data::pepxml::PeptideProphetResult::allNttProb, pwiz::data::pepxml::AnalysisResult::analysis, pwiz::data::pepxml::SearchHit::analysisResult, pwiz::data::pepxml::SpectrumQuery::assumedCharge, pwiz::data::pepxml::SpectrumQuery::endScan, pwiz::data::pepxml::SearchHit::peptide, pwiz::data::pepxml::AnalysisResult::peptideProphetResult, pwiz::data::pepxml::SpectrumQuery::precursorNeutralMass, pwiz::data::pepxml::PeptideProphetResult::probability, pwiz::data::pepxml::SpectrumQuery::retentionTimeSec, pwiz::data::pepxml::SearchResult::searchHit, pwiz::data::pepxml::SpectrumQuery::searchResult, and pwiz::data::pepxml::SpectrumQuery::startScan.

{
    SpectrumQuery spectrumQuery;
    spectrumQuery.startScan = startScan;
    spectrumQuery.endScan = endScan;
    spectrumQuery.precursorNeutralMass = precursorNeutralMass;
    spectrumQuery.assumedCharge = charge;
    spectrumQuery.retentionTimeSec = rt;

    SearchResult searchResult;

    SearchHit searchHit;
    searchHit.peptide = sequence;


    AnalysisResult analysisResult;
    analysisResult.analysis = "peptideprophet";

    PeptideProphetResult peptideProphetResult;
    peptideProphetResult.probability = score;
    peptideProphetResult.allNttProb.push_back(0);
    peptideProphetResult.allNttProb.push_back(0);
    peptideProphetResult.allNttProb.push_back(score);

    analysisResult.peptideProphetResult = peptideProphetResult;

    searchHit.analysisResult = analysisResult;
    searchResult.searchHit = searchHit;

    spectrumQuery.searchResult = searchResult;

    return spectrumQuery;

}

FeaturePtr makeFeature	(	double	mz,
		double	retentionTime
	)

Definition at line 165 of file PeptideMatcherTest.cpp.

References pwiz::chemistry::Ion::mz().

{
    FeaturePtr feature(new Feature());
    feature->mz = mz;
    feature->retentionTime = retentionTime;

    return feature;

}

void test

(

)

Definition at line 175 of file PeptideMatcherTest.cpp.

References pwiz::eharmony::PeptideMatcher::calculateDeltaMZDistribution(), pwiz::eharmony::PeptideMatcher::calculateDeltaRTDistribution(), e(), epsilon, pwiz::eharmony::PeptideMatcher::getDeltaMZParams(), pwiz::eharmony::PeptideMatcher::getDeltaRTParams(), pwiz::eharmony::PeptideMatcher::getMatches(), makeFeature(), makePeptideID_dataFetcher(), makeSpectrumQuery(), os_, samplePepXML_a, samplePepXML_b, unit_assert, unit_assert_equal, and pwiz::data::pepxml::SpectrumQuery::write().

{
    // construct test fdfs
    FeaturePtr a = makeFeature(1,2.1);
    FeaturePtr b = makeFeature(3,4.2);
    FeaturePtr c = makeFeature(5,6.4);
    FeaturePtr d = makeFeature(7,8.8);
    FeaturePtr e = makeFeature(9,1.9);

    vector<FeaturePtr> features_a;
    features_a.push_back(a);
    features_a.push_back(b);
    features_a.push_back(e);

    vector<FeaturePtr> features_b;
    features_b.push_back(c);
    features_b.push_back(d);
    features_b.push_back(e);

    Feature_dataFetcher fdf_a(features_a);
    Feature_dataFetcher fdf_b(features_b);

    // construct pidfs
    PidfPtr pidf_a = makePeptideID_dataFetcher(samplePepXML_a);
    PidfPtr pidf_b = makePeptideID_dataFetcher(samplePepXML_b);

    // construct PeptideMatcher
    //    DataFetcherContainer dfc(pidf_a, pidf_b, fdf_a, fdf_b);
    PeptideMatcher pm(pidf_a, pidf_b);
    PeptideMatchContainer pmc = pm.getMatches();
  
    // ensure that _matches attribute is filled in 
    unit_assert(pmc.size() != 0); 

    // and correctly:
    // construct the objects that should be in matches
    
    SpectrumQuery sq_a = makeSpectrumQuery(2.0,2.0,1,"BUCKLEMYSHOE",0.900,1,2);
    SpectrumQuery sq_b = makeSpectrumQuery(2.1,3.0,1,"BUCKLEMYSHOE",0.900,1,2);
    
    SpectrumQuery sq_c = makeSpectrumQuery(2.0,4.0,1,"ABIGFATHEN",0.900,9,10);
    SpectrumQuery sq_d = makeSpectrumQuery(2.2,2.0,1,"ABIGFATHEN",0.900,9,10);
    
    PeptideMatchContainer::iterator it = pmc.begin();
    if (os_)
        {
            *os_ << "\n[PeptideMatcherTest] Matches found:\n " << endl;
            ostringstream oss;
            XMLWriter writer(oss);
            PeptideMatchContainer::iterator it = pmc.begin();
            for(; it != pmc.end(); ++it)
                {
                    it->first->write(writer);
                    it->second->write(writer);
                  
                }           

            oss << "\n[PeptideMatcherTest] Looking for:\n " << endl;
            sq_a.write(writer);
            sq_b.write(writer);
            
            *os_ << oss.str() << endl;
        }

    // assert that known matches are found TODO fix
    /*
    unit_assert(find(pmc.begin(), pmc.end(), make_pair(sq_a, sq_b)) != pmc.end());
    unit_assert(find(pmc.begin(), pmc.end(), make_pair(sq_c, sq_d)) != pmc.end());
    */

     //  calculate deltaRtDistribution by hand
     double mean = 0.5;
     double stdev = 1.5;
 
     // and verify that it is correct
     pm.calculateDeltaRTDistribution();
    
     unit_assert_equal(pm.getDeltaRTParams().first, mean, 2 * numeric_limits<double>::epsilon());
     unit_assert_equal(pm.getDeltaRTParams().second, stdev, 2 * numeric_limits<double>::epsilon());

     // calculate deltaMZDistribution by  hand
     double mz_mean = -0.15;
     double mz_stdev = 0.05;

     // and verify that it is correct
     pm.calculateDeltaMZDistribution();

     unit_assert_equal(pm.getDeltaMZParams().first, mz_mean, 2 * numeric_limits<double>::epsilon());
     unit_assert_equal(pm.getDeltaMZParams().second, mz_stdev, 2 * numeric_limits<double>::epsilon());

}

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 267 of file PeptideMatcherTest.cpp.

References e(), os_, and test().

{
    try
        {
            if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
            test();

        }

    catch (std::exception& e)
        {
            cerr << e.what() << endl;
            return 1;

        }

    catch (...)
        {
            cerr << "Caught unknown exception.\n";
            return 1;

        }

}

---

Variable Documentation

ostream* os_ = 0

Definition at line 31 of file PeptideMatcherTest.cpp.

const char* samplePepXML_a = "</msms_pipeline_analysis>\n"

Definition at line 33 of file PeptideMatcherTest.cpp.

Referenced by test().

const char* samplePepXML_b = "</msms_pipeline_analysis>\n"

Definition at line 76 of file PeptideMatcherTest.cpp.

Referenced by test().