SpectrumList_MGF_Test.cpp File Reference

#include "SpectrumList_MGF.hpp"
#include "TextWriter.hpp"
#include "pwiz/utility/minimxml/XMLWriter.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Functions
void	test ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0
const char *	testMGF = "END IONS\n"

---

Function Documentation

void test

(

)

Definition at line 58 of file SpectrumList_MGF_Test.cpp.

References e(), pwiz::msdata::MSData::instrumentConfigurationPtrs, MS_base_peak_intensity, MS_base_peak_m_z, MS_charge_state, MS_LCQ_Deca, MS_ms_level, MS_scan_start_time, MS_selected_ion_m_z, MS_spectrum_title, MS_total_ion_current, os_, testMGF, unit_assert, unit_assert_equal, and write().

{
    if (os_) *os_ << "test()\n";

    if (os_) *os_ << "mgf:\n" << testMGF << endl;

    shared_ptr<istream> is(new istringstream(testMGF));

    // dummy would normally be read in from file

    MSData dummy;
    dummy.instrumentConfigurationPtrs.push_back(InstrumentConfigurationPtr(new InstrumentConfiguration("LCQDeca")));
    dummy.instrumentConfigurationPtrs.back()->cvParams.push_back(MS_LCQ_Deca);
    dummy.instrumentConfigurationPtrs.back()->userParams.push_back(UserParam("doobie", "420"));

    SpectrumListPtr sl = SpectrumList_MGF::create(is, dummy);

    if (os_)
    {
        TextWriter write(*os_);
        write(*sl);
        *os_ << endl;
    }

    // check easy functions

    unit_assert(sl.get());
    unit_assert(sl->size() == 2);
    unit_assert(sl->find("index=0") == 0);
    unit_assert(sl->find("index=1") == 1);

    // find the second spectrum by TITLE field
    IndexList list = sl->findSpotID("small.pwiz.0004.0004.2");
    unit_assert(list.size() == 1);
    unit_assert(list[0] == 1);

    // look for a non-existent TITLE field
    list.clear();
    list = sl->findSpotID("fake title string");
    unit_assert(list.size() == 0);

    // check scan 0

    unit_assert(sl->spectrumIdentity(0).index == 0);
    unit_assert(sl->spectrumIdentity(0).id == "index=0");
    unit_assert(sl->spectrumIdentity(0).sourceFilePosition != -1);

    SpectrumPtr s = sl->spectrum(0, false);

    unit_assert(s.get());
    unit_assert(s->id == "index=0");
    unit_assert(s->index == 0);
    unit_assert(s->sourceFilePosition != -1);
    unit_assert(s->cvParam(MS_spectrum_title).value == "small.pwiz.0003.0003.2");
    unit_assert(s->cvParam(MS_ms_level).valueAs<int>() == 2);
    unit_assert_equal(s->cvParam(MS_total_ion_current).valueAs<double>(), 64.992226, 1e-5);
    unit_assert_equal(s->cvParam(MS_base_peak_m_z).valueAs<double>(), 231.38884, 1e-5);
    unit_assert_equal(s->cvParam(MS_base_peak_intensity).valueAs<double>(), 26.545113, 1e-5);

    unit_assert(s->precursors.size() == 1);
    Precursor& precursor0 = s->precursors[0];
    unit_assert(precursor0.selectedIons.size() == 1);
    unit_assert_equal(precursor0.selectedIons[0].cvParam(MS_selected_ion_m_z).valueAs<double>(), 810.79, 1e-5);

    unit_assert(s->defaultArrayLength == 3);
    unit_assert(s->binaryDataArrayPtrs.empty());

    s = sl->spectrum(0, true);
    unit_assert(s->defaultArrayLength == 3);
    unit_assert(s->binaryDataArrayPtrs.size() == 2);
    unit_assert(!s->binaryDataArrayPtrs[0]->data.empty() && !s->binaryDataArrayPtrs[1]->data.empty());

    vector<MZIntensityPair> pairs;
    s->getMZIntensityPairs(pairs);

    if (os_)
    {
        *os_ << "scan 0:\n";
        copy(pairs.begin(), pairs.end(), ostream_iterator<MZIntensityPair>(*os_, "\n"));
        *os_ << endl;
    }


    // check scan 1

    unit_assert(sl->spectrumIdentity(1).index == 1);
    unit_assert(sl->spectrumIdentity(1).id == "index=1");

    s = sl->spectrum(1, true);
    unit_assert(s.get());
    unit_assert(s->id == "index=1");
    unit_assert(s->index == 1);
    unit_assert(s->sourceFilePosition != -1);
    unit_assert(s->cvParam(MS_spectrum_title).value == "small.pwiz.0004.0004.2");
    unit_assert(s->cvParam(MS_ms_level).valueAs<int>() == 2);
    unit_assert(s->scanList.scans.size() == 1);
    unit_assert_equal(s->scanList.scans[0].cvParam(MS_scan_start_time).timeInSeconds(), 123.456, 1e-5);

    unit_assert(s->precursors.size() == 1);
    Precursor& precursor1 = s->precursors[0];
    unit_assert(precursor1.selectedIons.size() == 1);
    unit_assert_equal(precursor1.selectedIons[0].cvParam(MS_selected_ion_m_z).valueAs<double>(), 837.34, 1e-5);
    unit_assert(precursor1.selectedIons[0].cvParam(MS_charge_state).value == "2");

    unit_assert(s->defaultArrayLength == 5);

    pairs.clear();
    s->getMZIntensityPairs(pairs);

    unit_assert(s->defaultArrayLength == pairs.size());

    if (os_)
    {
        *os_ << "scan 1:\n";
        copy(pairs.begin(), pairs.end(), ostream_iterator<MZIntensityPair>(*os_, "\n"));
        *os_ << endl;
    }
}

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

Definition at line 178 of file SpectrumList_MGF_Test.cpp.

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

{
    TEST_PROLOG(argc, argv)

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

    TEST_EPILOG
}

---

Variable Documentation

ostream* os_ = 0

Definition at line 36 of file SpectrumList_MGF_Test.cpp.

const char* testMGF = "END IONS\n"

Definition at line 38 of file SpectrumList_MGF_Test.cpp.

Referenced by test().