PeptideID_dataFetcherTest.cpp File Reference

#include "pwiz/utility/misc/unit.hpp"
#include "PeptideID_dataFetcher.hpp"
#include "Feature_dataFetcher.hpp"
#include "pwiz/utility/proteome/Ion.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include <iomanip>

Go to the source code of this file.

Classes
struct	IsSQ

Typedefs
typedef boost::shared_ptr < PeptideID_dataFetcher >	PidfPtr

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

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

---

Typedef Documentation

typedef boost::shared_ptr<PeptideID_dataFetcher> PidfPtr

Definition at line 35 of file PeptideID_dataFetcherTest.cpp.

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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 95 of file PeptideID_dataFetcherTest.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 xresult;
    xresult.probability = score;
    xresult.allNttProb.push_back(0);
    xresult.allNttProb.push_back(0);
    xresult.allNttProb.push_back(score);

    analysisResult.peptideProphetResult = xresult;

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

    spectrumQuery.searchResult = searchResult;
    
    return spectrumQuery;

}

PidfPtr makePeptideID_dataFetcher

(

const char *

samplePepXML

)

Definition at line 130 of file PeptideID_dataFetcherTest.cpp.

Referenced by test(), and testPeptideID_dataFetcherConstructor().

{

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

    return pidf;

}

void testPeptideID_dataFetcherConstructor

(

)

Definition at line 157 of file PeptideID_dataFetcherTest.cpp.

References makePeptideID_dataFetcher(), makeSpectrumQuery(), pwiz::chemistry::Ion::mz(), os_, samplePepXML, unit_assert, and pwiz::data::pepxml::SpectrumQuery::write().

Referenced by main().

{   
    if (os_)
        {
            *os_ << "\ntestPeptideID_dataFetcherConstructor() ... \n";
            *os_ << "\nSample pep.xml: \n";
            *os_ << samplePepXML << endl;

        }
    
    // make the PeptideID_dataFetcher from input pep.xml
    PidfPtr pidf = makePeptideID_dataFetcher(samplePepXML);

    // make the SpectrumQuery objects that we expect to be read into the PeptideID_dataFetcher 
    SpectrumQuery a = makeSpectrumQuery(1,2,1, "BUCKLEMYSHOE", 0.900, 1,2);  // mz, rt, charge, sequence, score, start scan, end scan
    SpectrumQuery b = makeSpectrumQuery(3,4,1,"SHUTTHEDOOR",0.900,3,4);
    SpectrumQuery c = makeSpectrumQuery(5,6,1,"PICKUPSTICKS",0.900,5,6);
    SpectrumQuery d = makeSpectrumQuery(7,8,1,"LAYTHEMSTRAIGHT",0.900,7,8);
    
    // Access SpectrumQuery objects that are in the PeptideID_dataFetcher at the coordinates we expect
    vector<boost::shared_ptr<SpectrumQuery> > sq_a = pidf->getSpectrumQueries(Ion::mz(1,1),2);
    vector<boost::shared_ptr<SpectrumQuery> > sq_b = pidf->getSpectrumQueries(Ion::mz(3,1),4);
    vector<boost::shared_ptr<SpectrumQuery> > sq_c = pidf->getSpectrumQueries(Ion::mz(5,1),6);
    vector<boost::shared_ptr<SpectrumQuery> > sq_d = pidf->getSpectrumQueries(Ion::mz(7,1),8);

    // Assert that all SpectrumQuery objects were found at expected coordinates
    unit_assert(find_if(sq_a.begin(), sq_a.end(),IsSQ(a)) != sq_a.end());
    unit_assert(find_if(sq_b.begin(), sq_b.end(),IsSQ(b)) != sq_b.end());
    unit_assert(find_if(sq_c.begin(), sq_c.end(),IsSQ(c)) != sq_c.end());
    unit_assert(find_if(sq_d.begin(), sq_d.end(),IsSQ(d)) != sq_d.end()); 

    if (os_)
        {
            *os_ << "\nSpectrumQuery objects read from sample pep.xml: \n";
            ostringstream oss;
            XMLWriter writer(oss);
            a.write(writer);
            b.write(writer);
            c.write(writer);
            d.write(writer);
            *os_ << oss.str() << endl;
        }

}

void testMerge

(

)

Definition at line 202 of file PeptideID_dataFetcherTest.cpp.

References pwiz::Bin< T >::getAllContents(), pwiz::eharmony::PeptideID_dataFetcher::getBin(), makeSpectrumQuery(), pwiz::eharmony::PeptideID_dataFetcher::merge(), pwiz::data::pepxml::MSMSPipelineAnalysis::msmsRunSummary, os_, pwiz::data::pepxml::SpectrumQuery::retentionTimeSec, pwiz::data::pepxml::MSMSRunSummary::spectrumQueries, and unit_assert.

{
    if (os_) *os_ << "\ntestMerge() ... \n" << endl;

    SpectrumQuery b = makeSpectrumQuery(1,2,1, "BUCKLEMYSHOE", 0.900, 1,2);
    SpectrumQuery c = makeSpectrumQuery(3,4,1, "SHUTTHEDOOR", 0.900, 3,4);

    vector<SpectrumQuery> v;
    v.push_back(b);

    vector<SpectrumQuery> v2;
    SpectrumQuery b2(b);
    b2.retentionTimeSec = 4000;
    v2.push_back(b2);
    v2.push_back(c);
        
    MSMSPipelineAnalysis mspa_fiat;
    mspa_fiat.msmsRunSummary.spectrumQueries = v;

    MSMSPipelineAnalysis mspa_chrysler;
    mspa_chrysler.msmsRunSummary.spectrumQueries = v2;

    PeptideID_dataFetcher fiat(mspa_fiat);
    PeptideID_dataFetcher chrysler(mspa_chrysler);
    
    fiat.merge(chrysler);
 
    // test that the merger correctly concatenated all SpectrumQuery objects
    //    vector<boost::shared_ptr<SpectrumQuery> > contents = fiat.getSpectrumQueries(Ion::mz(b.precursorNeutralMass, b.assumedCharge), b.retentionTimeSec);
    vector<boost::shared_ptr<SpectrumQuery> > contents = fiat.getBin().getAllContents();
    unit_assert(contents.size() == 2);
    unit_assert(**contents.begin() == b);
    unit_assert(*contents.back() == c);
    
    

}

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

Definition at line 240 of file PeptideID_dataFetcherTest.cpp.

References e(), os_, testMerge(), and testPeptideID_dataFetcherConstructor().

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

            testPeptideID_dataFetcherConstructor();
            testMerge();

        }

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

        }

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

        }

    return 0;

}

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Variable Documentation

ostream* os_ = 0

Definition at line 37 of file PeptideID_dataFetcherTest.cpp.

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

Definition at line 39 of file PeptideID_dataFetcherTest.cpp.

Referenced by test(), testIStream(), and testPeptideID_dataFetcherConstructor().