Feature2PeptideMatcherTest.cpp File Reference

#include "Feature2PeptideMatcher.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/data/misc/MinimumPepXML.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Classes
struct	PointsToSame

Functions
SpectrumQuery	makeSpectrumQuery (double precursorNeutralMass, double rt, int charge, string sequence, double score, int startScan, int endScan)
FeaturePtr	makeFeature (double mz, double retentionTime, string ms1_5, int charge=0)
void	test ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

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Function Documentation

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

Definition at line 44 of file Feature2PeptideMatcherTest.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 ppresult;
    ppresult.probability = score;
    ppresult.allNttProb.push_back(0);
    ppresult.allNttProb.push_back(0);
    ppresult.allNttProb.push_back(score);

    analysisResult.peptideProphetResult = ppresult;

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

    spectrumQuery.searchResult = searchResult;

    return spectrumQuery;

}

FeaturePtr makeFeature	(	double	mz,
		double	retentionTime,
		string	ms1_5,
		int	charge = 0
	)

Definition at line 80 of file Feature2PeptideMatcherTest.cpp.

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

Referenced by test(), testAdjustRT(), and testMerge().

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

    return feature;

}

void test

(

)

Definition at line 91 of file Feature2PeptideMatcherTest.cpp.

{

// TODO
// Goal is to test that we can catch all of the six ways in which we can be wrong or right in identifying a match:
 
// Ways to be right:
// A) Only one peptide within search radius of feature; peptide is correct and we call it correct; TP
// B) No peptides within search radius of feature; next nearest peptide is incorrect and we call it incorrect; TN
// C) More than one peptide within search radius of feature; one peptide is correct and we call it correct; TP; the rest are incorrect and we've called them incorrect; TN

// Ways to be wrong:
// D) Only one peptide within search radius of feature; peptide is incorrect and we call it correct; FP
// E) No peptides within search radius of feature; next nearest peptide is correct and we call it incorrect; FN;
// F) More than one peptide within search radius of feature; one peptide is correct and we call it incorrect; FN; the rest are incorrect and we've called one of them correct; FP

}

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

Definition at line 109 of file Feature2PeptideMatcherTest.cpp.

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

{
    try
        {
            if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
            if (os_) *os_ << "\nFeature2PeptideMatcherTest ... \n";
            test();

        }

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

        }

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

        }
}

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Variable Documentation

ostream* os_ = 0

Definition at line 33 of file Feature2PeptideMatcherTest.cpp.