SpectrumList_PrecursorRefineTest.cpp File Reference

#include "SpectrumList_PrecursorRefine.hpp"
#include "pwiz/data/msdata/MSDataFile.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "boost/filesystem/path.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include <cstring>

Go to the source code of this file.

Functions
void	verifyPrecursorMZ (const Spectrum &spectrum, double precursorMZ)
void	testPrecursorRefine (const bfs::path &datadir)
void	test (const bfs::path &datadir)
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

---

Function Documentation

void verifyPrecursorMZ	(	const Spectrum &	spectrum,
		double	precursorMZ
	)

Definition at line 42 of file SpectrumList_PrecursorRefineTest.cpp.

References pwiz::data::ParamContainer::cvParam(), e(), epsilon, pwiz::msdata::SpectrumIdentity::id, pwiz::msdata::SpectrumIdentity::index, MS_charge_state, MS_selected_ion_m_z, os_, pwiz::msdata::Spectrum::precursors, unit_assert, unit_assert_equal, and pwiz::data::CVParam::valueAs().

Referenced by testPrecursorRefine().

{
    unit_assert(!spectrum.precursors.empty()); 
    const Precursor& precursor = spectrum.precursors[0];
    unit_assert(!precursor.selectedIons.empty());
    const SelectedIon& selectedIon = precursor.selectedIons[0];

    double foo = selectedIon.cvParam(MS_selected_ion_m_z).valueAs<double>();

    const double epsilon = 1e-4;
    if (os_)
    {
        *os_ << "[verifyPrecursorMZ] " << spectrum.index << " " << spectrum.id << " "
             << precursorMZ << ": "
             << selectedIon.cvParam(MS_selected_ion_m_z).value << " " << selectedIon.cvParam(MS_charge_state).value << endl;
    }

    unit_assert_equal(selectedIon.cvParam(MS_selected_ion_m_z).valueAs<double>(), precursorMZ, epsilon);

}

void testPrecursorRefine

(

const bfs::path &

datadir

)

Definition at line 64 of file SpectrumList_PrecursorRefineTest.cpp.

References os_, pwiz::msdata::MSData::run, pwiz::msdata::Run::spectrumListPtr, unit_assert, and verifyPrecursorMZ().

Referenced by test().

{
    MSDataFile msd((datadir / "PrecursorRefineOrbi.mzML").string());
    
    unit_assert(msd.run.spectrumListPtr.get() && msd.run.spectrumListPtr->size()==51);
    if (os_) *os_ << "original spectra:\n";
    verifyPrecursorMZ(*msd.run.spectrumListPtr->spectrum(21), 747.37225);
    verifyPrecursorMZ(*msd.run.spectrumListPtr->spectrum(22), 614.867065);
    verifyPrecursorMZ(*msd.run.spectrumListPtr->spectrum(24), 547.2510);
    verifyPrecursorMZ(*msd.run.spectrumListPtr->spectrum(25), 533.2534);
    verifyPrecursorMZ(*msd.run.spectrumListPtr->spectrum(26), 401.22787);

    shared_ptr<SpectrumList_PrecursorRefine> spectrumListRecalculated(
        new SpectrumList_PrecursorRefine(msd));

    unit_assert(spectrumListRecalculated->size() == 51); 
    if (os_) *os_ << "recalculated spectra:\n";
    verifyPrecursorMZ(*spectrumListRecalculated->spectrum(21), 747.37078);
    verifyPrecursorMZ(*spectrumListRecalculated->spectrum(22), 614.86648);
    verifyPrecursorMZ(*spectrumListRecalculated->spectrum(24), 547.2507);
    verifyPrecursorMZ(*spectrumListRecalculated->spectrum(25), 533.2534);
    verifyPrecursorMZ(*spectrumListRecalculated->spectrum(26), 401.226957);
}

void test

(

const bfs::path &

datadir

)

Definition at line 89 of file SpectrumList_PrecursorRefineTest.cpp.

References testPrecursorRefine().

{
    testPrecursorRefine(datadir);
}

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

Definition at line 95 of file SpectrumList_PrecursorRefineTest.cpp.

References e(), os_, test(), TEST_EPILOG, TEST_FAILED, and TEST_PROLOG.

{
    TEST_PROLOG(argc, argv)

    try
    {
        bfs::path datadir = ".";

        for (int i=1; i<argc; i++)
        {
            if (!strcmp(argv[i],"-v")) 
                os_ = &cout;
            else
                // hack to allow running unit test from a different directory:
                // Jamfile passes full path to specified input file.
                // we want the path, so we can ignore filename
                datadir = bfs::path(argv[i]).branch_path(); 
        }   

        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
        test(datadir);
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}

---

Variable Documentation

ostream* os_ = 0

Definition at line 39 of file SpectrumList_PrecursorRefineTest.cpp.