C++ (Cpp) MassSpectrum::setPolarity Examples

Example #1

File: datafile.cpp Project: hermixy/qtplatz

//virtual
bool
datafile::getSpectrum( int fcn, size_t pos, adcontrols::MassSpectrum& ms, uint32_t objId ) const
{
	(void)fcn;

	try {
		EDAL::IMSSpectrumCollectionPtr pSpectra = pAnalysis_->GetMSSpectrumCollection();
		EDAL::IMSSpectrumPtr pSpectrum = pSpectra->GetItem( long(pos) + 1 ); // 1-origin

		if ( pSpectrum->Polarity == EDAL::SpectrumPolarity::IonPolarity_Negative )
			ms.setPolarity( adcontrols::MS_POLARITY::PolarityNegative );
		else if ( pSpectrum->Polarity == EDAL::SpectrumPolarity::IonPolarity_Positive )
			ms.setPolarity( adcontrols::MS_POLARITY::PolarityPositive );
		else
			ms.setPolarity( adcontrols::MS_POLARITY::PolarityIndeterminate );

		adcontrols::MSProperty prop = ms.getMSProperty();
		prop.setTimeSinceInjection( static_cast< unsigned long >( pSpectrum->RetentionTime /* sec */ * 1.0e6 ) ); // usec
        ms.setMSProperty( prop ); // <- end of prop set

		_variant_t vMasses, vIntens;
        if ( objId <= 1 ) {
			pSpectrum->GetMassIntensityValues( EDAL::SpectrumType_Profile, &vMasses, &vIntens );
			ms.setCentroid( adcontrols::CentroidNone );  // profile
        } else { // objId should be 2
			pSpectrum->GetMassIntensityValues( EDAL::SpectrumType_Line, &vMasses, &vIntens );
			ms.setCentroid( adcontrols::CentroidNative );
		}

		SafeArray sa_masses( vMasses );
        ms.resize( sa_masses.size() );
        ms.setMassArray( reinterpret_cast< const double *>( sa_masses.p() ) );
    
		SafeArray sa_intensities( vIntens );
        ms.setIntensityArray( reinterpret_cast< const double *>( sa_intensities.p() ) );

        ms.setAcquisitionMassRange( ms.getMass( 0 ), ms.getMass( ms.size() - 1 ) );

		return true;
	} catch(_com_error& ex ) {
		ADERROR() << std::wstring( ex.ErrorMessage() );
		return false;
	}
	return false;
}

Example #2

adcontrols::translate_state
DataInterpreter::translate_profile( adcontrols::MassSpectrum& ms
                                    , const char * data, size_t dsize
                                    , const char * meta, size_t msize
                                    , const adcontrols::MassSpectrometer& spectrometer
                                    , size_t idData ) const
{
	(void)idData;
    adportable::debug(__FILE__, __LINE__) << "translate_profile( dsize=" << dsize << ", msize=" << msize << ")";
    import_profile profile;
    import_continuum_massarray ma;
    
    const batchproc::MassSpectrometer* pSpectrometer = dynamic_cast< const batchproc::MassSpectrometer * >( &spectrometer );
    if ( pSpectrometer == 0 )
        return adcontrols::translate_error;

    if ( adportable::bzip2::is_a( data, dsize ) ) {

        std::string ar;
        adportable::bzip2::decompress( ar, data, dsize );
        adportable::debug(__FILE__, __LINE__) << "translate_profile deserialize import_profile w/ decompress";
        if ( ! adportable::serializer< import_profile >::deserialize( profile, ar.data(), ar.size() ) )
            return adcontrols::translate_error;

    } else {
        adportable::debug(__FILE__, __LINE__) << "translate_profile deserialize import_profile w/o decompress";
        if ( ! adportable::serializer< import_profile >::deserialize( profile, data, dsize ) ) 
            return adcontrols::translate_error;
    }

    if ( meta && msize ) {
        if ( adportable::bzip2::is_a( meta, msize ) ) {
            std::string ar;
            adportable::bzip2::decompress( ar, meta, msize );
            if ( ! adportable::serializer< import_continuum_massarray >::deserialize( ma, ar.data(), ar.size() ) )
                return adcontrols::translate_error;
        } else {
            if ( ! adportable::serializer< import_continuum_massarray >::deserialize( ma, meta, msize ) )
                return adcontrols::translate_error;
        }
    }

    adportable::debug(__FILE__, __LINE__) << "translate_profile checkpoint 3";
    const import_continuum_massarray& continuum_massarray = meta ? ma : pSpectrometer->continuum_massarray();
    
	ms.setMSProperty( profile.prop_ );
	ms.setPolarity( profile.polarity_ );
    ms.resize( profile.intensities_.size() );

    adportable::debug(__FILE__, __LINE__) << "translate_profile checkpoint 4";
    ms.setMassArray( continuum_massarray.masses_.data() );
    auto intens = profile.intensities_.data();
    for ( size_t i = 0; i < ms.size(); ++i )
        ms.setIntensity( i, *intens++ );

    adportable::debug(__FILE__, __LINE__) << "translate_profile checkpoint 5";
    ms.setAcquisitionMassRange( ms.getMass( 0 ), ms.getMass( ms.size() - 1 ) );

    adportable::debug(__FILE__, __LINE__) << "translate_profile checkpoint 6";

    return adcontrols::translate_complete;
}