ChromatogramList_mzML_Test.cpp File Reference

#include "ChromatogramList_mzML.hpp"
#include "Serializer_mzML.hpp"
#include "examples.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 (bool indexed)
void	test ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

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Function Documentation

void test

(

bool

indexed

)

Definition at line 40 of file ChromatogramList_mzML_Test.cpp.

References pwiz::msdata::MSData::dataProcessingPtrs, pwiz::msdata::Serializer_mzML::Config::indexed, pwiz::identdata::examples::initializeTiny(), os_, unit_assert, and pwiz::msdata::Serializer_mzML::write().

{
    if (os_) *os_ << "test(): indexed=\"" << boolalpha << indexed << "\"\n";

    MSData tiny;
    examples::initializeTiny(tiny);

    Serializer_mzML::Config config;
    config.indexed = indexed;
    Serializer_mzML serializer(config);  

    ostringstream oss;
    serializer.write(oss, tiny);

    if (os_) *os_ << "oss:\n" << oss.str() << endl;

    shared_ptr<istream> is(new istringstream(oss.str()));

    // dummy would normally be read in from file
  
    MSData dummy;

    // so we don't have any dangling references
    //dummy.instrumentPtrs.push_back(InstrumentPtr(new Instrument("LCQ_Deca")));
    dummy.dataProcessingPtrs.push_back(DataProcessingPtr(new DataProcessing("pwiz_processing")));
    dummy.dataProcessingPtrs.push_back(DataProcessingPtr(new DataProcessing("CompassXtract processing")));

    Index_mzML_Ptr index(new Index_mzML(is, dummy));
    ChromatogramListPtr sl = ChromatogramList_mzML::create(is, dummy, index);

    // check easy functions

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

    // check tic

    ChromatogramPtr s = sl->chromatogram(0); // read without binary data
    unit_assert(s.get());
    unit_assert(s->id == "tic");
    unit_assert(s->binaryDataArrayPtrs.empty());

    unit_assert(sl->chromatogramIdentity(0).index == 0);
    unit_assert(sl->chromatogramIdentity(0).id == "tic");

    s = sl->chromatogram(0, true); // read with binary data

    vector<TimeIntensityPair> pairs;
    s->getTimeIntensityPairs(pairs);
    unit_assert(pairs.size() == 15);
    for (int i=0; i<15; i++)
        unit_assert(pairs[i].time==i && pairs[i].intensity==15-i);

    // check sic

    s = sl->chromatogram(1, true);
    unit_assert(s.get());
    unit_assert(s->id == "sic");

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

    pairs.clear();
    s->getTimeIntensityPairs(pairs);
    unit_assert(pairs.size() == 10);
    for (int i=0; i<10; i++)
        unit_assert(pairs[i].time==i && pairs[i].intensity==(10-i));
}

void test

(

)

Definition at line 112 of file ChromatogramList_mzML_Test.cpp.

References test().

{
    bool indexed = true;
    test(indexed);

    indexed = false;
    test(indexed);
}

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

Definition at line 122 of file ChromatogramList_mzML_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
}

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Variable Documentation

ostream* os_ = 0

Definition at line 37 of file ChromatogramList_mzML_Test.cpp.