SpectrumList_mz5_Test.cpp File Reference

#include "pwiz/utility/misc/unit.hpp"
#include "SpectrumList_mz5.hpp"
#include "Serializer_mz5.hpp"
#include "examples.hpp"
#include "pwiz/utility/minimxml/XMLWriter.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "pwiz/utility/misc/Filesystem.hpp"

Go to the source code of this file.

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

Variables
ostream *	os_ = 0
const char *	testFilename = "SpectrumList_mz5_Test.mz5"

---

Function Documentation

void test

(

)

Definition at line 43 of file SpectrumList_mz5_Test.cpp.

References pwiz::msdata::MSData::dataProcessingPtrs, pwiz::msdata::MSData::fileDescription, pwiz::identdata::examples::initializeTiny(), pwiz::msdata::MSData::instrumentConfigurationPtrs, MS_full_scan, MS_ms_level, MS_positive_scan, pwiz::chemistry::Ion::mz(), pwiz::msdata::MSData::paramGroupPtrs, pwiz::msdata::Serializer_mz5::read(), pwiz::msdata::MSData::run, pwiz::msdata::FileDescription::sourceFilePtrs, pwiz::msdata::Run::spectrumListPtr, testFilename, unit_assert, and pwiz::msdata::Serializer_mz5::write().

{
    {
    MSData tiny;
    examples::initializeTiny(tiny);

    MSDataFile::WriteConfig writeConfig;
    Serializer_mz5 serializer(writeConfig);

    IterationListenerRegistry ilr;
    serializer.write(testFilename, tiny, &ilr);

    MSData dummy;
    serializer.read(testFilename, dummy);

    dummy.fileDescription.sourceFilePtrs.push_back(SourceFilePtr(new SourceFile("tiny1.yep")));
    dummy.fileDescription.sourceFilePtrs.push_back(SourceFilePtr(new SourceFile("tiny.wiff")));

    ParamGroupPtr pg1(new ParamGroup);
    pg1->id = "CommonMS1SpectrumParams";
    pg1->cvParams.push_back(MS_positive_scan);
    pg1->cvParams.push_back(MS_full_scan);
    dummy.paramGroupPtrs.push_back(pg1);

    ParamGroupPtr pg2(new ParamGroup);
    pg2->id = "CommonMS2SpectrumParams";
    pg2->cvParams.push_back(MS_positive_scan);
    pg2->cvParams.push_back(MS_full_scan);
    dummy.paramGroupPtrs.push_back(pg2);

    // so we don't have any dangling references
    dummy.instrumentConfigurationPtrs.push_back(InstrumentConfigurationPtr(
            new InstrumentConfiguration("LCQ Deca")));
    dummy.dataProcessingPtrs.push_back(DataProcessingPtr(new DataProcessing(
            "CompassXtract processing")));

    SpectrumListPtr sl = dummy.run.spectrumListPtr;

    // check easy functions

    unit_assert(sl.get());
    unit_assert(sl->size() == 5);
    unit_assert(sl->find("scan=19") == 0);
    IndexList indexList = sl->findNameValue("scan", "19");
    unit_assert(indexList.size() == 1 && indexList[0] == 0);
    unit_assert(sl->find("scan=20") == 1);
    indexList = sl->findNameValue("scan", "20");
    unit_assert(indexList.size() == 1 && indexList[0] == 1);
    unit_assert(sl->find("scan=21") == 2);
    indexList = sl->findNameValue("scan", "21");
    unit_assert(indexList.size() == 1 && indexList[0] == 2);
    unit_assert(sl->find("sample=1 period=1 cycle=23 experiment=1") == 4);
    indexList = sl->findNameValue("sample", "1");
    unit_assert(indexList.size() == 1 && indexList[0] == 4);
    indexList = sl->findNameValue("period", "1");
    unit_assert(indexList.size() == 1 && indexList[0] == 4);
    indexList = sl->findNameValue("cycle", "23");
    unit_assert(indexList.size() == 1 && indexList[0] == 4);
    indexList = sl->findNameValue("experiment", "1");
    unit_assert(indexList.size() == 1 && indexList[0] == 4);

    unit_assert(sl->findSpotID("A1").empty());
    IndexList spotIndexList = sl->findSpotID("A1,42x42,4242x4242");
    unit_assert(spotIndexList.size() == 1);
    unit_assert(spotIndexList[0] == 4);

    // check scan 19

    SpectrumPtr s = sl->spectrum(0); // read without binary data
    unit_assert(s.get());
    unit_assert(s->id == "scan=19");
    unit_assert(s->spotID.empty());
    unit_assert(s->cvParam(MS_ms_level).valueAs<int> () == 1);
    unit_assert(s->binaryDataArrayPtrs.empty());

    unit_assert(sl->spectrumIdentity(0).index == 0);
    unit_assert(sl->spectrumIdentity(0).id == "scan=19");
    unit_assert(sl->spectrumIdentity(0).spotID.empty());

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

    vector < MZIntensityPair > pairs;
    s->getMZIntensityPairs(pairs);
    unit_assert(pairs.size() == 15);
    for (int i = 0; i < 15; i++)
        unit_assert(pairs[i].mz == i && pairs[i].intensity == 15 - i);

    unit_assert(s->scanList.scans.size() == 1);
    unit_assert(s->paramGroupPtrs.size() == 1);
    unit_assert(s->paramGroupPtrs.back()->id == "CommonMS1SpectrumParams");
    unit_assert(s->paramGroupPtrs.back()->cvParams.size() == 2);

    // check scan 20

    s = sl->spectrum(1, true);
    unit_assert(s.get());
    unit_assert(s->id == "scan=20");
    unit_assert(s->spotID.empty());
    unit_assert(s->cvParam(MS_ms_level).valueAs<int> () == 2);

    unit_assert(sl->spectrumIdentity(1).index == 1);
    unit_assert(sl->spectrumIdentity(1).id == "scan=20");
    unit_assert(sl->spectrumIdentity(1).spotID.empty());

    pairs.clear();
    s->getMZIntensityPairs(pairs);
    unit_assert(pairs.size() == 10);
    for (int i = 0; i < 10; i++)
        unit_assert(pairs[i].mz == 2 * i && pairs[i].intensity == (10 - i) * 2);

    unit_assert(s->scanList.scans.size() == 1);
    unit_assert(s->paramGroupPtrs.size() == 1);
    unit_assert(s->paramGroupPtrs.back()->id == "CommonMS2SpectrumParams");
    unit_assert(s->paramGroupPtrs.back()->cvParams.size() == 2);

    // check scan 22 (MALDI)
    s = sl->spectrum(4, true);
    unit_assert(s.get());
    unit_assert(s->id == "sample=1 period=1 cycle=23 experiment=1");
    unit_assert(s->spotID == "A1,42x42,4242x4242");
    unit_assert(s->cvParam(MS_ms_level).valueAs<int> () == 1);

    unit_assert(sl->spectrumIdentity(4).index == 4);
    unit_assert(sl->spectrumIdentity(4).id == "sample=1 period=1 cycle=23 experiment=1");
    unit_assert(sl->spectrumIdentity(4).spotID == "A1,42x42,4242x4242");

    }
    bfs::remove(testFilename);
}

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

Definition at line 173 of file SpectrumList_mz5_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 39 of file SpectrumList_mz5_Test.cpp.

const char* testFilename = "SpectrumList_mz5_Test.mz5"

Definition at line 40 of file SpectrumList_mz5_Test.cpp.