AlignedChromatogram.cpp

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#include "stdafx.h"
#include "AlignedChromatogram.h"


using namespace kome::operation;


#include <crtdbg.h>
#ifdef _DEBUG
    #define new new( _NORMAL_BLOCK, __FILE__, __LINE__ )
    #define malloc( s ) _malloc_dbg( s, _NORMAL_BLOCK, __FILE__, __LINE__ )
#endif    // _DEBUG



// constructor
AlignedChromatogram::AlignedChromatogram( kome::objects::Chromatogram& org, Alignment* align )
        : kome::objects::Chromatogram( org.getSample() ), m_org( org ) {
    // initialize
    m_align = align;
    if( m_align == NULL ) {
        m_align = &( Alignment::getDefaultAlignment() );
    }

    setOrgChromatogram( org.getOrgChromatogram() );
}

// destructor
AlignedChromatogram::~AlignedChromatogram() {
}

// on get xy data
void AlignedChromatogram::onGetXYData( kome::core::XYData* const xyData ) {
    // check the parameter
    if( xyData == NULL ) {
        return;
    }

    // get xy data
    kome::core::DataPoints dps;
    m_org.getXYData( &dps, false );

    // add points
    for( unsigned int i = 0; i < dps.getLength(); i++ ) {
        const double x = m_align->convertRt( dps.getX( i ), m_org.getMz() );
        const double y = dps.getY( i );

        xyData->addPoint( x, y );
    }
}

// on get spectra
void AlignedChromatogram::onGetSpectra(
        kome::objects::DataSet& spectra,
        const double startRt,
        const double endRt,
        const kome::objects::SearchType startSearch,
        const kome::objects::SearchType endSearch
) {
    // get xy data
    kome::core::DataPoints dps0;
    kome::core::DataPoints dps1;
    kome::core::DataPoints dps2;

    m_org.getXYData( &dps0, false );
    onGetXYData( &dps1 );

    // add aligned xy data
    if( dps0.getLength() > 0 ) {
        dps2.reserve( dps0.getLength() );
    }

    for( unsigned int i = 0; i < dps0.getLength(); i++ ) {
        dps2.addPoint( dps1.getX( 0 ), dps0.getX( i ) );
    }

    // get org RT
    const double orgStartRt = kome::numeric::Interpolation::linear( dps2, startRt );
    const double orgEndRt = kome::numeric::Interpolation::linear( dps2, endRt );

    // get spectra
    m_org.getSpectra( spectra, orgStartRt, orgEndRt, startSearch, endSearch );
}

// on get mass
double AlignedChromatogram::onGetMass( const unsigned int index ) {
    return m_org.getMass( index );
}

// on get MS stage
int AlignedChromatogram::onGetMsStage( const unsigned int index ) {
    return m_org.getMsStage( index );
}

// on get precursor
double AlignedChromatogram::onGetPrecursor( const unsigned int index ) {
    return m_org.getPrecursor( index );
}