kome::objects::Peaks2D Class Reference

2-dimentional peaks More...

#include <Peaks2D.h>

Inheritance diagram for kome::objects::Peaks2D:

Collaboration diagram for kome::objects::Peaks2D:

Public Member Functions
	Peaks2D ()
	constructor
	Peaks2D (const Peaks2D &peaks)
	copy constructor More...
virtual	~Peaks2D ()
	destructor
Peaks2D &	operator= (const Peaks2D &other)
	substitution operator More...
Peak2DElement *	createPeak (const double rt, const double startRt, const double endRt, const double mz, const double startMz, const double endMz, const double intensity)
	creates new peak element More...
Peak2DElement *	createPeak (const double rt, const double mz, const double intensity)
	creates new peak element More...
void	clearPeaks ()
	clears peaks
void	removePeak (Peak2DElement *peak)
	removes peak More...
void	removePeak (const unsigned int idx)
	removes peak More...
PeaksCluster2D *	createCluster ()
	creates cluster More...
unsigned int	getNumberOfClusters ()
	gets the number of clusters More...
PeaksCluster2D *	getCluster (const unsigned int idx)
	gets cluster More...
void	clearClusters ()
	clears clusters
void	removeCluster (PeaksCluster2D *cluster)
	removes cluster More...
void	removeCluster (const unsigned int idx)
	removes cluster More...
void	setDataId (const int id)
	sets the data ID More...
int	getDataId ()
	gets the data ID More...
Public Member Functions inherited from kome::objects::Peaks2DArray
	Peaks2DArray ()
	constructor
virtual	~Peaks2DArray ()
	destructor
int	issueId (Peak2DElement *peak2dElement)
	to issue the peak2d id More...
Peak2DElement *	getPeakById (int id)
	gets peak element by peak2d id More...
unsigned int	getNumberOfPeaks ()
	gets the number of peaks More...
Peak2DElement *	getPeak (const unsigned int idx)
	gets peak element More...
int	searchPeak (Peak2DElement *peak)
	searches peak More...
void	sortByRt (const bool desc)
	sorts peaks by RT More...
void	sortByMz (const bool desc)
	sorts peaks by m/z More...
void	sortByIntensity (const bool desc)
	sorts peaks by intensity param desc descending order flag

Protected Attributes
std::vector< PeaksCluster2D * >	m_clusters
int	m_dataId
Protected Attributes inherited from kome::objects::Peaks2DArray
std::vector< Peak2DElement * >	m_peaks

Additional Inherited Members
Static Protected Member Functions inherited from kome::objects::Peaks2DArray
static bool	lessRt (Peak2DElement *p0, Peak2DElement *p1, bool desc)
	compares peaks to sort by RT More...
static bool	lessMz (Peak2DElement *p0, Peak2DElement *p1, bool desc)
	compares peaks to sort by m/z More...
static bool	lessIntensity (Peak2DElement *p0, Peak2DElement *p1, bool desc)
	compares peaks to sort by intensity More...

Detailed Description

2-dimentional peaks

Definition at line 32 of file Peaks2D.h.

Constructor & Destructor Documentation

kome::objects::Peaks2D::Peaks2D

(

const Peaks2D &

peaks

)

copy constructor

Parameters

[in]

peaks

copy source

Definition at line 38 of file Peaks2D.cpp.

                                       {
    // create clusters
    std::map< PeaksCluster2D*, PeaksCluster2D* > clusterMap;
    clusterMap[ NULL ] = NULL;

    for( unsigned int i = 0; i < peaks.m_clusters.size(); i++ ) {
        // source cluster
        PeaksCluster2D* src = peaks.m_clusters[ i ];

        // new cluster
        PeaksCluster2D* cluster = new PeaksCluster2D();
        m_clusters.push_back( cluster );
        clusterMap[ src ] = cluster;

        cluster->setRt( src->getRt() );
        cluster->setRtRange( src->getStartRt(), src->getEndRt() );      
        cluster->setMz( src->getMz() );
        cluster->setMzRange( src->getStartMz(), src->getEndMz() );
        cluster->setIntensity( src->getIntensity() );
    }

    // create peaks
    m_peaks.clear();
    for( unsigned int i = 0; i < peaks.m_peaks.size(); i++ ) {
        // source peak
        Peak2DElement* src = peaks.m_peaks[ i ];

        // new peak
        Peak2DElement* peak = new Peak2DElement( this );
        m_peaks.push_back( peak );

        peak->setRt( src->getRt(), src->getStartRt(), src->getEndRt() );
        peak->setMz( src->getMz(), src->getStartMz(), src->getEndMz() );
        peak->setIntensity( src->getIntensity() );

        PeaksCluster2D* cluster = clusterMap[ src->getCluster() ];
        if( cluster != NULL ) {
            cluster->addPeak( peak );
        }
    }

    // data ID
    m_dataId = peaks.m_dataId;
}

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Member Function Documentation

PeaksCluster2D * kome::objects::Peaks2D::createCluster

(

)

creates cluster

Returns

new cluster object

Definition at line 248 of file Peaks2D.cpp.

                                       {
    PeaksCluster2D* cluster = new PeaksCluster2D();
    m_clusters.push_back( cluster );

    return cluster;
}

Peak2DElement * kome::objects::Peaks2D::createPeak	(	const double	rt,
		const double	startRt,
		const double	endRt,
		const double	mz,
		const double	startMz,
		const double	endMz,
		const double	intensity
	)

creates new peak element

Parameters

[in]	rt	RT
[in]	startRt	start RT
[in]	endRt	end RT
[in]	mz	m/z
[in]	startMz	start m/z
[in]	endMz	end m/z
[in]	intensity	intensity

Returns

new peak element object

Definition at line 138 of file Peaks2D.cpp.

  {
    // create peak
    Peak2DElement* peak = new Peak2DElement( this );
    m_peaks.push_back( peak );

    // set
    peak->setRt( rt, startRt, endRt );
    peak->setMz( mz, startMz, endMz );
    peak->setIntensity( intensity );

    return peak;
}

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Peak2DElement * kome::objects::Peaks2D::createPeak	(	const double	rt,
		const double	mz,
		const double	intensity
	)

creates new peak element

Parameters

[in]	rt	RT
[in]	mz	m/z
[in]	intensity	intensity

Returns

new peak element object

Definition at line 196 of file Peaks2D.cpp.

  {
    // create peak
    Peak2DElement* peak = createPeak( rt, rt, rt, mz, mz, mz, intensity );
    return peak;
}

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PeaksCluster2D * kome::objects::Peaks2D::getCluster

(

const unsigned int

idx

)

gets cluster

Parameters

[in]

idx

cluster index

Returns

cluster (If NULL, the index is illegal.)

Definition at line 261 of file Peaks2D.cpp.

                                                            {
    if( idx >= m_clusters.size() ) {
        return NULL;
    }
    return m_clusters[ idx ];
}

int kome::objects::Peaks2D::getDataId

(

)

gets the data ID

Returns

data ID

Definition at line 310 of file Peaks2D.cpp.

                       {
    return m_dataId;
}

unsigned int kome::objects::Peaks2D::getNumberOfClusters

(

)

gets the number of clusters

Returns

the number of clusters

Definition at line 256 of file Peaks2D.cpp.

                                          {
    return m_clusters.size();
}

Peaks2D & kome::objects::Peaks2D::operator=

(

const Peaks2D &

other

)

substitution operator

Parameters

[in]

other

source peaks

Returns

copied peaks object

Definition at line 90 of file Peaks2D.cpp.

                                                  {
    // create clusters
    std::map< PeaksCluster2D*, PeaksCluster2D* > clusterMap;
    clusterMap[ NULL ] = NULL;

    for( unsigned int i = 0; i < other.m_clusters.size(); i++ ) {
        // source cluster
        PeaksCluster2D* src = other.m_clusters[ i ];

        // new cluster
        PeaksCluster2D* cluster = new PeaksCluster2D();
        m_clusters.push_back( cluster );
        clusterMap[ src ] = cluster;

        cluster->setRt( src->getRt() );
        cluster->setRtRange( src->getStartRt(), src->getEndRt() );      
        cluster->setMz( src->getMz() );
        cluster->setMzRange( src->getStartMz(), src->getEndMz() );
        cluster->setIntensity( src->getIntensity() );
    }

    // create peaks
    m_peaks.clear();
    for( unsigned int i = 0; i < other.m_peaks.size(); i++ ) {
        // source peak
        Peak2DElement* src = other.m_peaks[ i ];

        // new peak
        Peak2DElement* peak = new Peak2DElement( this );
        m_peaks.push_back( peak );

        peak->setRt( src->getRt(), src->getStartRt(), src->getEndRt() );
        peak->setMz( src->getMz(), src->getStartMz(), src->getEndMz() );
        peak->setIntensity( src->getIntensity() );

        PeaksCluster2D* cluster = clusterMap[ src->getCluster() ];
        if( cluster != NULL ) {
            cluster->addPeak( peak );
        }
    }

    // data ID
    m_dataId = other.m_dataId;

    return *this;
}

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void kome::objects::Peaks2D::removeCluster

(

PeaksCluster2D *

cluster

)

removes cluster

Parameters

[in]

cluster

cluster to be removed

Definition at line 277 of file Peaks2D.cpp.

                                                     {
    // search 
    int idx = -1;
    for( unsigned int i = 0; i < m_clusters.size() && idx < 0; i++ ) {
        if( cluster == m_clusters[ i ] ) {
            idx = (int)i;
        }
    }

    // remove
    if( idx >= 0 ) {
        removeCluster( idx );
    }
}

void kome::objects::Peaks2D::removeCluster

(

const unsigned int

idx

)

removes cluster

Parameters

[in]

idx

cluster index

Definition at line 293 of file Peaks2D.cpp.

                                                    {
    // check
    if( idx >= m_clusters.size() ) {
        return;
    }

    // remove
    delete m_clusters[ idx ];
    m_clusters.erase( m_clusters.begin() + idx );
}

void kome::objects::Peaks2D::removePeak

(

Peak2DElement *

peak

)

removes peak

Parameters

[in]

peak

peak to be removed

Definition at line 215 of file Peaks2D.cpp.

                                              {
    // search
    int idx = -1;
    for( unsigned int i = 0; i < m_peaks.size() && idx < 0 ; i++ ) {
        if( peak == m_peaks[ i ] ) {
            idx = (int)i;
        }
    }

    // remove
    if( idx >= 0 ) {
        removePeak( idx );
    }
}

void kome::objects::Peaks2D::removePeak

(

const unsigned int

idx

)

removes peak

Parameters

[in]

idx

peak index

Definition at line 231 of file Peaks2D.cpp.

                                                 {
    // check
    if( idx >= m_peaks.size() ) {
        return;
    }

    // delete
    kome::objects::Peak2DElement* peak = m_peaks[ idx ];
    kome::objects::PeaksCluster2D* cluster = peak->getCluster();
    if( cluster != NULL ) {
        cluster->removePeak( peak );
    }
    delete peak;
    m_peaks.erase( m_peaks.begin() + idx );
}

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void kome::objects::Peaks2D::setDataId

(

const int

id

)

sets the data ID

Parameters

[in]

id

data ID

Definition at line 305 of file Peaks2D.cpp.

                                      {
    m_dataId = id;
}

Member Data Documentation

std::vector< PeaksCluster2D* > kome::objects::Peaks2D::m_clusters

protected

clusters

Definition at line 64 of file Peaks2D.h.

int kome::objects::Peaks2D::m_dataId

protected

data ID

Definition at line 68 of file Peaks2D.h.

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The documentation for this class was generated from the following files:

• DataObjects/Peaks2D.h
• DataObjects/Peaks2D.cpp