NeighborJoinerTest.cpp File Reference

#include "NeighborJoiner.hpp"
#include "pwiz/utility/misc/unit.hpp"

Go to the source code of this file.

Functions
boost::shared_ptr< SpectrumQuery >	makeSpectrumQuery (double precursorNeutralMass, double rt, int charge, string sequence, double score, int startScan, int endScan)
void	test ()
int	main ()

---

Function Documentation

boost::shared_ptr<SpectrumQuery> makeSpectrumQuery	(	double	precursorNeutralMass,
		double	rt,
		int	charge,
		string	sequence,
		double	score,
		int	startScan,
		int	endScan
	)

Definition at line 34 of file NeighborJoinerTest.cpp.

References pwiz::data::pepxml::PeptideProphetResult::allNttProb, pwiz::data::pepxml::AnalysisResult::analysis, pwiz::data::pepxml::SearchHit::analysisResult, pwiz::data::pepxml::SearchHit::peptide, pwiz::data::pepxml::AnalysisResult::peptideProphetResult, pwiz::data::pepxml::PeptideProphetResult::probability, and pwiz::data::pepxml::SearchResult::searchHit.

{
    boost::shared_ptr<SpectrumQuery> spectrumQuery(new 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;

}

void test

(

)

Definition at line 68 of file NeighborJoinerTest.cpp.

References makeSpectrumQuery(), and unit_assert.

{
    vector<boost::shared_ptr<SpectrumQuery> > testSpectrumQueries;
    testSpectrumQueries.push_back(makeSpectrumQuery(550.82, 83.46, 3, "MAHTOMEDI", .95, 612, 651));
    testSpectrumQueries.push_back(makeSpectrumQuery(02.139, 02.142, 3, "CAMBRIDGE", .95, 617, 857));
    testSpectrumQueries.push_back(makeSpectrumQuery(904.04, 913.60, 3, "MAHTOMEDI", .95, 310, 805));
    testSpectrumQueries.push_back(makeSpectrumQuery(537.17, 53.703, 3, "MAHTOMEDI", .96, 608, 715));

    PidfPtr four(new PeptideID_dataFetcher(testSpectrumQueries));
    testSpectrumQueries.erase(testSpectrumQueries.begin());
    testSpectrumQueries.erase(testSpectrumQueries.begin());
    PidfPtr two(new PeptideID_dataFetcher(testSpectrumQueries));
    testSpectrumQueries.erase(testSpectrumQueries.begin());
    PidfPtr one(new PeptideID_dataFetcher(testSpectrumQueries));

    boost::shared_ptr<Feature_dataFetcher> dummy_fdf(new Feature_dataFetcher());

    boost::shared_ptr<AMTContainer> cuatro(new AMTContainer());
    cuatro->_pidf = four;
    cuatro->_fdf = dummy_fdf;
    boost::shared_ptr<AMTContainer> dos(new AMTContainer());
    dos->_pidf = two;
    dos->_fdf = dummy_fdf;
    boost::shared_ptr<AMTContainer> uno(new AMTContainer());
    uno->_pidf = one;
    uno->_fdf = dummy_fdf;

    vector<boost::shared_ptr<AMTContainer> > testEntries;
    testEntries.push_back(cuatro);
    testEntries.push_back(dos);
    testEntries.push_back(uno);

    NeighborJoiner neighborJoiner(testEntries);
    boost::shared_ptr<NumberOfMS2IDs> numpep(new NumberOfMS2IDs());

    neighborJoiner.addDistanceAttribute(numpep);    
    neighborJoiner.calculateDistanceMatrix();
    neighborJoiner.joinNearest();

    // make the merger that we are looking for
    dos->merge(*uno);

    unit_assert(neighborJoiner._rowEntries.back() == *dos);
    unit_assert(neighborJoiner._columnEntries.back() == *dos);
    
    neighborJoiner.calculateDistanceMatrix(); //recalculate given the recent merger
    neighborJoiner.joinNearest();

    // make the merger that we are looking for
    cuatro->merge(*dos);

    unit_assert(neighborJoiner._rowEntries.back() == *cuatro);
    unit_assert(neighborJoiner._columnEntries.back() == *cuatro);

}

int main

(

)

Definition at line 124 of file NeighborJoinerTest.cpp.

References test().

{
    test();
    return 0;

}