kome::objects::DataSet Class Reference

one or more spectra management class More...

#include <DataSet.h>

Inheritance diagram for kome::objects::DataSet:

Collaboration diagram for kome::objects::DataSet:

Public Member Functions
	DataSet ()
	constructor
	DataSet (DataGroupNode *group)
	constructor More...
virtual	~DataSet ()
	destructor
Sample *	getSample ()
	gets sample More...
DataGroupNode *	getGroup ()
	gets spectrum group More...
unsigned int	getNumberOfSpectra ()
	gets the number of spectra More...
Spectrum *	getSpectrum (const unsigned int index)
	gets the number of spectra More...
unsigned int	getNumberOfChromatograms ()
	gets the number of chromatograms More...
Chromatogram *	getChromatogram (const unsigned int index)
	gets chroamtogram More...
virtual void	sortSpectra ()
	sorts spectra in retention time order
virtual void	clearSpectra ()
	clears spectra
virtual void	addSpectrum (Spectrum *spec)
	adds spectrum to group More...
virtual void	removeSpectrum (Spectrum *spec)
	removes spectrum More...
virtual void	insertSpectrum (Spectrum *spec, const int idx)
	inserts spectrum More...
virtual void	clearChromatograms ()
	clears chromatograms
virtual void	addChromatogram (Chromatogram *chrom)
	adds chromatogram More...
virtual void	removeChromatogram (Chromatogram *chrom)
	removes chromatogram More...
virtual void	insertChromatogram (Chromatogram *chrom, const int idx)
	inserts chromatogram More...

Static Protected Member Functions
static bool	lessSpectrum (Spectrum *spec0, Spectrum *spec1)
	compare to sort spectra More...

Protected Attributes
Sample *	m_sample
DataGroupNode *	m_group
std::vector< Spectrum * >	m_spectra
std::vector< Chromatogram * >	m_chroms

Detailed Description

one or more spectra management class

Definition at line 31 of file DataSet.h.

Constructor & Destructor Documentation

kome::objects::DataSet::DataSet

(

DataGroupNode *

group

)

constructor

Parameters

[in]

group

spectrum group

Definition at line 39 of file DataSet.cpp.

                                       {
    m_group = group;
    m_sample = ( m_group == NULL ) ? NULL : group->getSample();
}

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Member Function Documentation

void kome::objects::DataSet::addChromatogram ( Chromatogram *  chrom )

virtual

adds chromatogram

Parameters

[in]

chrom

chromatogram

Definition at line 217 of file DataSet.cpp.

                                                   {
    insertChromatogram( chrom, (int)m_chroms.size() );
}

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void kome::objects::DataSet::addSpectrum ( Spectrum *  spec )

virtual

adds spectrum to group

Parameters

[in]

spec

spectrum object to be added

Definition at line 167 of file DataSet.cpp.

                                          {
    insertSpectrum( spec, (int)m_spectra.size() );
}

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Chromatogram * kome::objects::DataSet::getChromatogram

(

const unsigned int

index

)

gets chroamtogram

Parameters

[in]

index

chromatogram index

Returns

chromatogram (If NULL, the index is illegal.)

Definition at line 146 of file DataSet.cpp.

                                                                 {
    // check the index
    if( index >= m_chroms.size() ) {
        return NULL;
    }
    return m_chroms[ index ];
}

DataGroupNode * kome::objects::DataSet::getGroup

(

)

gets spectrum group

Returns

spectrum group

Definition at line 65 of file DataSet.cpp.

                                 {
    // check the member
    if( m_group != NULL ) {
        return m_group;
    }

    // groups
    std::set< DataGroupNode* > groupSet;

    for( unsigned int i = 0; i < m_spectra.size(); i++ ) {
        Spectrum* spec = m_spectra[ i ];
        DataGroupNode* g = spec->getGroup();
        if( g == NULL ) {
            return NULL;
        }
        else {
            groupSet.insert( g );
        }
    }

    for( unsigned int i = 0; i < m_chroms.size(); i++ ) {
        Chromatogram* chrom = m_chroms[ i ];
        DataGroupNode* g = chrom->getGroup();
        if( g == NULL ) {
            return NULL;
        }
        else {
            groupSet.insert( g );
        }
    }

    // common group
    DataGroupNode* group = NULL;
    for( std::set< DataGroupNode* >::iterator it = groupSet.begin();
            it != groupSet.end(); it++ ) {
        DataGroupNode* g = *it;

        if( group == NULL ) {
            group = g;
        }
        else {
            while( group != NULL && group->getLevel() > g->getLevel() ) {
                group = group->getParentGroup();
            }
            while( g != NULL && g->getLevel() > group->getLevel() ) {
                g = g->getParentGroup();
            }

            while( group != NULL && g != NULL && g != group ) {
                group = group->getParentGroup();
                g = g->getParentGroup();
            }

            if( group == NULL || g == NULL ) {
                return NULL;
            }
        }
    }

    return group;
}

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unsigned int kome::objects::DataSet::getNumberOfChromatograms

(

)

gets the number of chromatograms

Returns

the number of chromatograms

Definition at line 141 of file DataSet.cpp.

                                               {
    return m_chroms.size();
}

unsigned int kome::objects::DataSet::getNumberOfSpectra

(

)

gets the number of spectra

Returns

the number of spectra

Definition at line 128 of file DataSet.cpp.

                                         {
    return m_spectra.size();
}

Sample * kome::objects::DataSet::getSample

(

)

gets sample

Returns

sample

Definition at line 49 of file DataSet.cpp.

                           {
    // check the member
    if( m_sample != NULL ) {
        return m_sample;
    }

    // group
    DataGroupNode* group = getGroup();
    if( group == NULL ) {
        return NULL;
    }

    return group->getSample();
}

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Spectrum * kome::objects::DataSet::getSpectrum

(

const unsigned int

index

)

gets the number of spectra

Returns

the numbe of spectra

Definition at line 133 of file DataSet.cpp.

                                                         {
    if( index >= m_spectra.size() ) {
        return NULL;
    }
    return m_spectra[ index ];
}

void kome::objects::DataSet::insertChromatogram ( Chromatogram *  chrom, const int  idx  )

virtual

inserts chromatogram

Parameters

[in]	chrom	chromatogram to be inserted
[in]	idx	insert position

Reimplemented in kome::objects::DataGroupNode.

Definition at line 239 of file DataSet.cpp.

                                                                     {
    // check the parameter
    if( chrom == NULL ) {
        return;
    }

    // check group
    bool flg = false;
    DataGroupNode* group = chrom->getGroup();
    while( group != NULL && !flg ) {
        if( m_group == group ) {
            flg = true;
        }
        group = group->getParentGroup();
    }

    // insert
    if( m_group == NULL || flg ) {
        m_chroms.insert( m_chroms.begin() + idx, chrom );
    }
}

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void kome::objects::DataSet::insertSpectrum ( Spectrum *  spec, const int  idx  )

virtual

inserts spectrum

Parameters

[in]	spec	spectrum to be inserted.
[in]	idx	insert position

Reimplemented in kome::objects::DataGroupNode.

Definition at line 189 of file DataSet.cpp.

                                                            {
    // check the parameter
    if( spec == NULL ) {
        return;
    }

    // check group
    bool flg = false;
    DataGroupNode* group = spec->getGroup();
    while( group != NULL && !flg ) {
        if( m_group == group ) {
            flg = true;
        }
        group = group->getParentGroup();
    }

    // add
    if( m_group == NULL || flg ) {
        m_spectra.insert( m_spectra.begin() + idx, spec );
    }
}

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static bool kome::objects::DataSet::lessSpectrum ( Spectrum *  spec0, Spectrum *  spec1  )

staticprotected

compare to sort spectra

Parameters

[in]	spec0	spectrum object to be compared
[in]	spec1	spectrum object to compare

Returns

If spec0 sorts before spec1, this method returns true.

Definition at line 262 of file DataSet.cpp.

                                                             {
    // @date 2013.11.11 <Del> M.Izumi ->
    //const int s0 = spec0->getScanNumber();
    //const int s1 = spec1->getScanNumber();
    //if( s0 >= 0 && s1 >= 0 ) {
    //  if( s0 < s1 ) {
    //      return true;
    //  }
    //  return false;
    //}
    // @date 2013.11.11 <Del> M.Izumi <-

    // RT
    const double rt0 = spec0->getRt();
    const double rt1 = spec1->getRt();

    if( rt0 < rt1 ) {
        return true;
    }
    else if( rt0 > rt1 ) {
        return false;
    }

    return false;
}

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void kome::objects::DataSet::removeChromatogram ( Chromatogram *  chrom )

virtual

removes chromatogram

Parameters

[in]

chrom

chromatogram to be removed

Definition at line 222 of file DataSet.cpp.

                                                      {
    // search
    int idx = -1;
    for( unsigned int i = 0; i < m_chroms.size() && idx < 0; i++ ) {
        kome::objects::Chromatogram* tmp = m_chroms[ i ];
        if( tmp == chrom ) {
            idx = (int)i;
        }
    }

    // remove
    if( idx >= 0 ) {
        m_chroms.erase( m_chroms.begin() + idx );
    }
}

void kome::objects::DataSet::removeSpectrum ( Spectrum *  spec )

virtual

removes spectrum

Parameters

[in]

spec

spectrum to be removed

Definition at line 172 of file DataSet.cpp.

                                             {
    // search
    int idx = -1;
    for( unsigned int i = 0; i < m_spectra.size() && idx < 0; i++ ) {
        Spectrum* tmp = m_spectra[ i ];
        if( tmp == spec ) {
            idx = (int)i;
        }
    }

    // remove
    if( idx >= 0 ) {
        m_spectra.erase( m_spectra.begin() + idx );
    }
}

Member Data Documentation

std::vector< Chromatogram* > kome::objects::DataSet::m_chroms

protected

chromatograms

Definition at line 63 of file DataSet.h.

DataGroupNode* kome::objects::DataSet::m_group

protected

group

Definition at line 57 of file DataSet.h.

Sample* kome::objects::DataSet::m_sample

protected

sample

Definition at line 54 of file DataSet.h.

std::vector< Spectrum* > kome::objects::DataSet::m_spectra

protected

spectrum array

Definition at line 60 of file DataSet.h.

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

• DataObjects/DataSet.h
• DataObjects/DataSet.cpp