DataFetcherContainerTest.cpp File Reference

#include "DataFetcherContainer.hpp"
#include "pwiz/data/misc/MinimumPepXML.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "boost/shared_ptr.hpp"

Go to the source code of this file.

Typedefs
typedef boost::shared_ptr < DataFetcherContainer >	DfcPtr

Functions
void	testAdjustRT ()
void	testGetAnchors ()
void	testWarpRT ()
int	main (int argc, char *argv[])

---

Typedef Documentation

typedef boost::shared_ptr<DataFetcherContainer> DfcPtr

Definition at line 39 of file DataFetcherContainerTest.cpp.

---

Function Documentation

void testAdjustRT

(

)

Definition at line 236 of file DataFetcherContainerTest.cpp.

References makeFeature(), makeSpectrumQuery(), os_, pwiz::data::pepxml::SpectrumQuery::retentionTimeSec, and unit_assert.

Referenced by main().

{
    DfcPtr dfc = makeDataFetcherContainer();

    FeaturePtr ab = makeFeature(3.00727, 3.5);
    ab->id = "99";
    ab->charge = 1;
    FeatureSequenced fs_ab;
    fs_ab.feature = ab;
    fs_ab.ms1_5="";
    fs_ab.ms2="RAG";
        
    SpectrumQuery a =  makeSpectrumQuery(2, 2, 1, "KRH", 5, 6, 7);
    SpectrumQuery b =  makeSpectrumQuery(2, 4, 1, "RAG", 7, 8, 9);

    vector<boost::shared_ptr<FeatureSequenced> > f_prime = dfc->_fdf_a->getBin().getAllContents();
    
    if (os_)
        {
            ostringstream oss;
            XMLWriter writer(oss);
            vector<boost::shared_ptr<FeatureSequenced> >::iterator it = f_prime.begin();
            for(; it != f_prime.end(); ++it) 
                {
                    (*it)->feature->write(writer);
                    oss << (*it)->ms1_5 << endl;
                    oss << (*it)->ms2 << endl;

                }

            fs_ab.feature->write(writer);
            oss << fs_ab.ms1_5 << endl;
            oss << fs_ab.ms2 << endl;
            *os_ << oss.str() << endl;

        }

    // did the feature sequence get assigned as expected?
    unit_assert(find_if(f_prime.begin(), f_prime.end(), IsObject<FeatureSequenced>(fs_ab)) != f_prime.end());

    // did the peptide retention time get assigned as expected?
    b.retentionTimeSec = 3.5;    

    vector<boost::shared_ptr<SpectrumQuery> > sq_prime = dfc->_pidf_a->getBin().getAllContents();

    if (os_)
        {
            ostringstream oss;
            XMLWriter writer(oss);
            vector<boost::shared_ptr<SpectrumQuery> >::iterator it = sq_prime.begin();
            for(; it != sq_prime.end(); ++it)
                {                   
                    (*it)->write(writer);

                }

            *os_ << oss.str() << endl;

        }

    unit_assert(find_if(sq_prime.begin(), sq_prime.end(), IsObject<SpectrumQuery>(b)) != sq_prime.end());

    // we also expect a's retention time to be set to that of feature ab, since it is the only option and therefore the best
    a.retentionTimeSec = 3.5;
    unit_assert(find_if(sq_prime.begin(), sq_prime.end(), IsObject<SpectrumQuery>(a)) != sq_prime.end());

    // were the appropriate flags set?
    unit_assert(dfc->_pidf_a->getRtAdjustedFlag());
    unit_assert(dfc->_fdf_a->getMS2LabeledFlag());

}

void testGetAnchors

(

)

Definition at line 308 of file DataFetcherContainerTest.cpp.

References pwiz::eharmony::Default, and unit_assert.

Referenced by main().

{
    PidfPtr pidf_a(makeBigPeptideID_dataFetcher());
    PidfPtr pidf_b(makeBigBadPeptideID_dataFetcher());
    
    DataFetcherContainer dfc(pidf_a, pidf_b, FdfPtr(new Feature_dataFetcher()), FdfPtr(new Feature_dataFetcher()));
    dfc.warpRT(Default, 2); // get every 2nd anchor, using default tolerance of 100 seconds   
    
    vector<pair<double, double> > trueAnchors;
    trueAnchors.push_back(make_pair(2,2));

    unit_assert(trueAnchors == dfc.anchors());
    
    trueAnchors.clear();

    dfc.warpRT(Default,2, 110); // get every 2nd anchor, using higher tolerance of 110 seconds
    trueAnchors.push_back(make_pair(2, 105));
    trueAnchors.push_back(make_pair(2, 2));

    unit_assert(trueAnchors == dfc.anchors());
                            
}

void testWarpRT

(

)

Definition at line 358 of file DataFetcherContainerTest.cpp.

References epsilon, pwiz::eharmony::Linear, and unit_assert_equal.

Referenced by main().

{
    DataFetcherContainer dfc(makeWarpTestPidfA(), makeWarpTestPidfB(), makeWarpTestFdfA(), makeWarpTestFdfB());
    dfc.adjustRT();
    dfc.warpRT(Linear, 2);

    vector<double> pidf_a_rts = getRTs(dfc._pidf_a);
    vector<double> pidf_b_rts = getRTs(dfc._pidf_b);
    vector<double> fdf_a_rts = getRTs(dfc._fdf_a);
    vector<double> fdf_b_rts = getRTs(dfc._fdf_b);
    
    vector<double> a_truth;
    a_truth.push_back(0.49899999999999);
    a_truth.push_back(1.74599200000000);
    a_truth.push_back(3.00300000000000);
    
    vector<double> b_truth;
    b_truth.push_back(-0.7580079999999);
    b_truth.push_back(2.99799200000000);
    b_truth.push_back(5.51200800000000);

    vector<double>::iterator par = pidf_a_rts.begin();
    vector<double>::iterator far = fdf_a_rts.begin();
    vector<double>::iterator at = a_truth.begin();

    for(; at != a_truth.end(); ++at, ++far, ++par) 
        {
            //            unit_assert_equal(*par, *at, epsilon);
            //unit_assert_equal(*far, *at, epsilon);

        }

    vector<double>::iterator pbr = pidf_b_rts.begin();
    vector<double>::iterator fbr = fdf_b_rts.begin();
    vector<double>::iterator bt = b_truth.begin();

    for(; bt != b_truth.end(); ++bt, ++fbr, ++pbr)
        {
            unit_assert_equal(*pbr, *bt, epsilon);
            unit_assert_equal(*fbr, *bt, epsilon);

        }
    
}

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

Definition at line 403 of file DataFetcherContainerTest.cpp.

References e(), os_, testAdjustRT(), testGetAnchors(), and testWarpRT().

{

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

            return 0;
        }
    catch (exception& e)
        {
            cerr << e.what() << endl;
        }
    catch (...)
        {
            cerr << "Caught unknown exception.\n";
        }

    return 1;
}