Serializer_MSn_Test.cpp File Reference

#include "Serializer_MSn.hpp"
#include "Serializer_mzML.hpp"
#include "Diff.hpp"
#include "TextWriter.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "boost/iostreams/positioning.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include <cstring>

Go to the source code of this file.

Functions
void	initializeTinyMS1 (MSData &msd)
void	initializeTinyMS2 (MSData &msd)
void	testWriteReadMS1 (const MSData &msd)
void	testWriteReadBMS1 (const MSData &msd)
void	testWriteReadCMS1 (const MSData &msd)
void	testWriteReadMS2 (const MSData &msd)
void	testWriteReadBMS2 (const MSData &msd)
void	testWriteReadCMS2 (const MSData &msd)
void	testWriteRead ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

---

Function Documentation

void initializeTinyMS1

(

MSData &

msd

)

Definition at line 39 of file Serializer_MSn_Test.cpp.

References pwiz::msdata::Spectrum::defaultArrayLength, pwiz::msdata::FileDescription::fileContent, pwiz::msdata::MSData::fileDescription, pwiz::msdata::Spectrum::getIntensityArray(), pwiz::msdata::Spectrum::getMZArray(), pwiz::msdata::SpectrumIdentity::id, pwiz::msdata::SpectrumIdentity::index, MS_base_peak_intensity, MS_base_peak_m_z, MS_centroid_spectrum, MS_highest_observed_m_z, MS_lowest_observed_m_z, MS_MS2_file, MS_ms_level, MS_MSn_spectrum, MS_number_of_counts, MS_scan_number_only_nativeID_format, MS_scan_start_time, MS_total_ion_current, pwiz::msdata::MSData::run, pwiz::msdata::Spectrum::scanList, pwiz::msdata::ScanList::scans, pwiz::data::ParamContainer::set(), pwiz::msdata::Spectrum::setMZIntensityArrays(), pwiz::msdata::FileDescription::sourceFilePtrs, pwiz::msdata::Run::spectrumListPtr, and UO_second.

Referenced by testWriteRead().

{
    FileContent& fc = msd.fileDescription.fileContent;
    fc.set(MS_MSn_spectrum);
    fc.set(MS_centroid_spectrum);

    SourceFilePtr sourceFile(new SourceFile);
    sourceFile->set(MS_scan_number_only_nativeID_format);
    sourceFile->set(MS_MS2_file);
    msd.fileDescription.sourceFilePtrs.push_back(sourceFile);

    shared_ptr<SpectrumListSimple> spectrumList(new SpectrumListSimple);
    msd.run.spectrumListPtr = spectrumList;
    spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));

    Spectrum& s20 = *spectrumList->spectra[0];
    s20.id = "scan=1";
    s20.index = 0;

    s20.set(MS_MSn_spectrum);
    s20.set(MS_ms_level, 1);

    s20.set(MS_centroid_spectrum);
    s20.set(MS_lowest_observed_m_z, 0);
    s20.set(MS_highest_observed_m_z, 18);
    s20.set(MS_base_peak_m_z, 0);
    s20.set(MS_base_peak_intensity, 20);
    s20.set(MS_total_ion_current, 110);

        s20.scanList.scans.push_back(Scan());
    Scan& s20scan = s20.scanList.scans.back();
    s20scan.set(MS_scan_start_time, 4, UO_second);

    s20.setMZIntensityArrays(vector<double>(), vector<double>(), MS_number_of_counts);
    vector<double>& s20_mz = s20.getMZArray()->data;
    vector<double>& s20_intensity = s20.getIntensityArray()->data;

    for (int i=0; i<10; i++)
        s20_mz.push_back(i*2);

    for (int i=0; i<10; i++)
        s20_intensity.push_back((10-i)*2);

    s20.defaultArrayLength = s20_mz.size();

} // initializeTinyMS1()

void initializeTinyMS2

(

MSData &

msd

)

Definition at line 86 of file Serializer_MSn_Test.cpp.

References pwiz::msdata::Spectrum::defaultArrayLength, pwiz::msdata::FileDescription::fileContent, pwiz::msdata::MSData::fileDescription, pwiz::msdata::Spectrum::getIntensityArray(), pwiz::msdata::Spectrum::getMZArray(), pwiz::msdata::SpectrumIdentity::id, pwiz::msdata::SpectrumIdentity::index, pwiz::msdata::Precursor::isolationWindow, MS_base_peak_intensity, MS_base_peak_m_z, MS_centroid_spectrum, MS_highest_observed_m_z, MS_isolation_window_target_m_z, MS_lowest_observed_m_z, MS_m_z, MS_MS2_file, MS_ms_level, MS_MSn_spectrum, MS_number_of_counts, MS_possible_charge_state, MS_scan_number_only_nativeID_format, MS_scan_start_time, MS_selected_ion_m_z, MS_total_ion_current, pwiz::msdata::Spectrum::precursors, pwiz::msdata::MSData::run, pwiz::msdata::Spectrum::scanList, pwiz::msdata::ScanList::scans, pwiz::msdata::Precursor::selectedIons, pwiz::data::ParamContainer::set(), pwiz::msdata::Spectrum::setMZIntensityArrays(), pwiz::msdata::FileDescription::sourceFilePtrs, pwiz::msdata::Run::spectrumListPtr, and UO_second.

Referenced by testWriteRead().

{
    FileContent& fc = msd.fileDescription.fileContent;
    fc.set(MS_MSn_spectrum);
    fc.set(MS_centroid_spectrum);

    SourceFilePtr sourceFile(new SourceFile);
    sourceFile->set(MS_scan_number_only_nativeID_format);
    sourceFile->set(MS_MS2_file);
    msd.fileDescription.sourceFilePtrs.push_back(sourceFile);

    shared_ptr<SpectrumListSimple> spectrumList(new SpectrumListSimple);
    msd.run.spectrumListPtr = spectrumList;
    spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));

    Spectrum& s20 = *spectrumList->spectra[0];
    s20.id = "scan=1";
    s20.index = 0;

    s20.set(MS_MSn_spectrum);
    s20.set(MS_ms_level, 2);

    s20.set(MS_centroid_spectrum);
    s20.set(MS_lowest_observed_m_z, 0);
    s20.set(MS_highest_observed_m_z, 18);
    s20.set(MS_base_peak_m_z, 0);
    s20.set(MS_base_peak_intensity, 20);
    s20.set(MS_total_ion_current, 110);

    s20.precursors.resize(1);
    Precursor& precursor = s20.precursors.front();
    precursor.selectedIons.resize(1);
    precursor.selectedIons[0].set(MS_selected_ion_m_z, 445.34, MS_m_z);
    precursor.selectedIons[0].set(MS_possible_charge_state, 2);
    precursor.isolationWindow.set(MS_isolation_window_target_m_z, 445.34, MS_m_z);

    s20.scanList.scans.push_back(Scan());
    Scan& s20scan = s20.scanList.scans.back();
    s20scan.set(MS_scan_start_time, 4, UO_second);

    s20.setMZIntensityArrays(vector<double>(), vector<double>(), MS_number_of_counts);
    vector<double>& s20_mz = s20.getMZArray()->data;
    vector<double>& s20_intensity = s20.getIntensityArray()->data;

    for (int i=0; i<10; i++)
        s20_mz.push_back(i*2);

    for (int i=0; i<10; i++)
        s20_intensity.push_back((10-i)*2);

    s20.defaultArrayLength = s20_mz.size();

} // initializeTinyMS2()

void testWriteReadMS1

(

const MSData &

msd

)

Definition at line 141 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_MS1, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

{
    Serializer_MSn serializer(MSn_Type_MS1);

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

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

    MSData msd2;
    shared_ptr<istream> iss(new istringstream(oss.str()));
    serializer.read(iss, msd2);

    DiffConfig config;
    config.ignoreMetadata = true;
    Diff<MSData, DiffConfig> diff(msd, msd2, config);

    if (os_ && diff) *os_ << diff << endl; 
    unit_assert(!diff);
}

void testWriteReadBMS1

(

const MSData &

msd

)

Definition at line 162 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreDataProcessing, pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_BMS1, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

{
    Serializer_MSn serializer(MSn_Type_BMS1);

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

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

    MSData msd2;
    shared_ptr<istream> iss(new istringstream(oss.str()));
    serializer.read(iss, msd2);

    DiffConfig config;
    config.ignoreMetadata = true;
    config.ignoreDataProcessing = true;
    Diff<MSData, DiffConfig> diff(msd, msd2, config);
    if (os_ && diff) *os_ << diff << endl; 
    unit_assert(!diff);
}

void testWriteReadCMS1

(

const MSData &

msd

)

Definition at line 183 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreDataProcessing, pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_CMS1, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

{
    Serializer_MSn serializer(MSn_Type_CMS1);

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

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

    MSData msd2;
    shared_ptr<istream> iss(new istringstream(oss.str()));
    serializer.read(iss, msd2);

    DiffConfig config;
    config.ignoreMetadata = true;
    config.ignoreDataProcessing = true;
    Diff<MSData, DiffConfig> diff(msd, msd2, config);
    if (os_ && diff) *os_ << diff << endl; 
    unit_assert(!diff);
}

void testWriteReadMS2

(

const MSData &

msd

)

Definition at line 204 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_MS2, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

{
    Serializer_MSn serializer(MSn_Type_MS2);

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

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

    MSData msd2;
    shared_ptr<istream> iss(new istringstream(oss.str()));
    serializer.read(iss, msd2);

    DiffConfig config;
    config.ignoreMetadata = true;
    Diff<MSData, DiffConfig> diff(msd, msd2, config);
    if (os_ && diff) *os_ << diff << endl; 
    unit_assert(!diff);
}

void testWriteReadBMS2

(

const MSData &

msd

)

Definition at line 224 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreDataProcessing, pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_BMS2, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

{
    Serializer_MSn serializer(MSn_Type_BMS2);

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

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

    MSData msd2;
    shared_ptr<istream> iss(new istringstream(oss.str()));
    serializer.read(iss, msd2);

    DiffConfig config;
    config.ignoreMetadata = true;
    config.ignoreDataProcessing = true;
    Diff<MSData, DiffConfig> diff(msd, msd2, config);
    if (os_ && diff) *os_ << diff << endl; 
    unit_assert(!diff);
}

void testWriteReadCMS2

(

const MSData &

msd

)

Definition at line 245 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreDataProcessing, pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_CMS2, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

{
    Serializer_MSn serializer(MSn_Type_CMS2);

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

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

    MSData msd2;
    shared_ptr<istream> iss(new istringstream(oss.str()));
    serializer.read(iss, msd2);

    DiffConfig config;
    config.ignoreMetadata = true;
    config.ignoreDataProcessing = true;
    Diff<MSData, DiffConfig> diff(msd, msd2, config);
    if (os_ && diff) *os_ << diff << endl; 
    unit_assert(!diff);
}

void testWriteRead

(

)

Definition at line 266 of file Serializer_MSn_Test.cpp.

References initializeTinyMS1(), initializeTinyMS2(), testWriteReadBMS1(), testWriteReadBMS2(), testWriteReadCMS1(), testWriteReadCMS2(), testWriteReadMS1(), and testWriteReadMS2().

{
    MSData msd1, msd2;

    initializeTinyMS1(msd1);
    initializeTinyMS2(msd2);

    testWriteReadMS1(msd1);
    testWriteReadBMS1(msd1);
    testWriteReadCMS1(msd1);
    testWriteReadMS2(msd2);
    testWriteReadBMS2(msd2);
    testWriteReadCMS2(msd2);
}

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

Definition at line 282 of file Serializer_MSn_Test.cpp.

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

{
    TEST_PROLOG(argc, argv)

    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
        testWriteRead();
    }
    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 Serializer_MSn_Test.cpp.