spectrum group chromatogram class More...

#include <SpectraChromatogram.h>

Inheritance diagram for kome::objects::SpectraChromatogram:

Collaboration diagram for kome::objects::SpectraChromatogram:

Public Member Functions
	SpectraChromatogram (DataSet &dataSet, bool bProces=false)
	constructor More...

virtual	~SpectraChromatogram ()
	destructor

DataSet &	getMemberSpectra ()
	gets spectra More...

void	setMzRange (const double minMz, const double maxMz)
	sets m/z range More...

void	setMinMz (const double mz)
	sets minimum value of m/z range More...

void	setMaxMz (const double mz)
	sets maximum value of m/z range More...

double	getMinMz ()
	gets minimum value of m/z range More...

double	getMaxMz ()
	gets maximum value of m/z range More...

void	setRtRange (const double minRt, const double maxRt)
	sets RT range More...

void	setMinRt (const double rt)
	sets minimum value of RT range More...

void	setMaxRt (const double rt)
	sets maximum value of RT range More...

double	getMinRt ()
	gets minimum value of RT range More...

double	getMaxRt ()
	gets maximum value of RT range More...

void	setFilter (const unsigned char filter)
	sets filter More...

unsigned char	getFilter ()
	gets filter More...

void	setTIC ()
	sets Total Ion SpectraChromatogram mode

void	setBPC ()
	sets Base Peak SpectraChromatogram mode

bool	isTIC ()
	judges whether chromatogram mode is TIC (Total Ion SpectraChromatogram) More...

bool	isBPC ()
	judges whether chromatogram mode is BPC (Base Peak SpectraChromatogram) More...

Public Member Functions inherited from kome::objects::Chromatogram
	Chromatogram (Sample *sample)
	constructor More...

virtual	~Chromatogram ()
	destructor

void	setOperationFlag (const bool op)
	sets the operation flag value More...

bool	getOperationFlag ()
	gets the operation flag value More...

void	setId (int id)
	sets chromatogram id More...

int	getId ()
	gets chromatogram id More...

Sample *	getSample ()
	gets sample More...

void	setName (const char *name)
	sets chromatogram name More...

const char *	getName ()
	gets chromatogram name More...

void	setMz (const double mz)
	sets m/z More...

double	getMz ()
	gets m/z More...

void	setGroup (DataGroupNode *group)
	sets spectrum group More...

DataGroupNode *	getGroup ()
	gets spectrum group More...

void	setIcon (const char *icon)
	sets icon name More...

const char *	getIcon ()
	gets icon name More...

void	setTitle (const char *title)
	sets title More...

const char *	getTitle ()
	gets title More...

kome::core::Properties &	getProperties ()
	gets properties More...

kome::core::Properties &	getUserProperties ()
	gets user properties More...

void	setAutoCreated (const bool autoCreated=true)
	sets auto created flag More...

bool	isAutoCreated ()
	gets auto created flag value More...

void	setVisible (const bool visible)
	sets the visible flag More...

bool	isVisible ()
	gets the visible flag value More...

void	setOrgChromatogram (Chromatogram *chrom)
	sets original chromatogram More...

Chromatogram *	getOrgChromatogram ()
	gets original chromatogram More...

void	setQ1 (const double q1)
	sets the Q1 Mass More...

double	getQ1 ()
	gets the Q1 Mass More...

void	setQ3 (const double q3)
	sets the Q3 Mass More...

double	getQ3 ()
	gets the Q3 Mass More...

kome::core::XYData *	getXYData ()
	gets xy data from data manager More...

void	deleteXYData ()
	deletes xy data of data manager

void	getXYData (kome::core::XYData *const xyData, const bool op)
	gets chromatogram data points More...

Spectrum *	searchSpectrum (const double rt, const SearchType search=SEARCH_NEAR)
	searches spectrum More...

void	getSpectra (DataSet &dataSet, const double startRt, const double endRt, const SearchType startSearch=SEARCH_NEAR, const SearchType endSearch=SEARCH_NEAR)
	get spectra in specified RT range More...

double	getMass (const unsigned int index)
	gets mass More...

int	getMsStage (const unsigned int index)
	gets MS stage More...

double	getPrecursor (const unsigned int index)
	gets precursor mass More...

void	getProperties (kome::core::Properties &properties)
	gets spectrum and spectrum group properties More...

void	getUserProperties (kome::core::Properties &userProperties)
	gets chromatogram and chromatogram group user properties More...

Protected Member Functions
void	setTitle ()
	sets title

void	getIntensities ()
	gets intensities

void	getMemberSpectra (std::vector< Spectrum * > &spectra)
	gets spectra of chromatogram point More...

int	searchSpectrumIndex (std::vector< Spectrum * > &spectra, const double rt, SearchType search)
	searches spectrum More...

virtual void	onGetXYData (kome::core::XYData *const xyData)
	This method is called by getXYData method (override method) More...

virtual void	onGetSpectra (DataSet &spectra, const double startRt, const double endRt, const SearchType startSearch, const SearchType endSearch)
	This method is called by searchSpectrum or getDataSet method (overriede method) More...

virtual double	onGetMass (const unsigned int index)
	This method is called by getMass method (override method) More...

virtual int	onGetMsStage (const unsigned int index)
	This method is called by getMsStage method (override method) More...

virtual double	onGetPrecursor (const unsigned int index)
	This method is called by getPrecursor method (override method) More...

Protected Attributes
DataSet *	m_spectra

double	m_minMz

double	m_maxMz

double	m_minRt

double	m_maxRt

unsigned char	m_filter

bool	m_tic

bool	m_proc

Protected Attributes inherited from kome::objects::Chromatogram
Sample *	m_sample

DataGroupNode *	m_group

std::string	m_name

double	m_mz

std::string	m_icon

std::string	m_title

kome::core::Properties	m_props

kome::core::Properties	m_userProps

bool	m_autoCreated

bool	m_visible

Chromatogram *	m_orgChrom

bool	m_op

int	m_chromId

double	m_q1

double	m_q3

Static Protected Attributes
static const unsigned char	m_msFilters []

Static Protected Attributes inherited from kome::objects::Chromatogram
static std::vector< std::string >	m_commonProps

Additional Inherited Members
Static Public Member Functions inherited from kome::objects::Chromatogram
static bool	isCommonProperty (const char *key)
	check whther the specified property key is common property or not More...

Detailed Description

spectrum group chromatogram class

Definition at line 29 of file SpectraChromatogram.h.

Constructor & Destructor Documentation

kome::objects::SpectraChromatogram::SpectraChromatogram	(	DataSet &	dataSet,
		bool	bProces = `false`
	)

constructor

Parameters

[in]	dataSet	spectra data set
[in]	bProces	Processing data is used if it is true.

Definition at line 50 of file SpectraChromatogram.cpp.

         : Chromatogram( dataSet.getGroup() == NULL ? NULL : dataSet.getGroup()->getSample() ) {
     // initialize
     m_minMz = -1.0;
     m_maxMz = -1.0;
     m_minRt = -1.0;
     m_maxRt = -1.0;
     m_filter = 0xff;
     m_tic = true;
     
     m_proc = bProces; // add flg @date 2012.10.03 <Add> M.Izumi
 
     m_spectra = &dataSet;
     
     m_group = dataSet.getGroup();
     setTitle();
 }

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Member Function Documentation

unsigned char kome::objects::SpectraChromatogram::getFilter ( )

gets filter

Returns

filter

The least significant bit is the ms1 filter.
The second least significant bit is the ms2 filter.
...
The most least significant bit is the ms8 or more filter.

Definition at line 152 of file SpectraChromatogram.cpp.

                                              {
     return m_filter;
 }

double kome::objects::SpectraChromatogram::getMaxMz ( )

gets maximum value of m/z range

Returns: maximum value of m/z range (If m/z range doesn't have upper bound, this method returns negative number.)

Definition at line 107 of file SpectraChromatogram.cpp.

                                      {
     return m_maxMz;
 }

double kome::objects::SpectraChromatogram::getMaxRt ( )

gets maximum value of RT range

Returns: maximum value of RT range (If RT range doesn't have upper bound, this method returns negative number.)

Definition at line 139 of file SpectraChromatogram.cpp.

                                      {
     return m_maxRt;
 }

DataSet & kome::objects::SpectraChromatogram::getMemberSpectra ( )

gets spectra

Returns: spectra

Definition at line 73 of file SpectraChromatogram.cpp.

                                                {
     return *m_spectra;
 }

void kome::objects::SpectraChromatogram::getMemberSpectra ( std::vector< Spectrum * > & spectra )

protected

gets spectra of chromatogram point

Parameters

[out] spectra spectrum array object to store spectra

Definition at line 185 of file SpectraChromatogram.cpp.

                                                                             {
     // get xy data
     for( unsigned int i = 0; i < m_spectra->getNumberOfSpectra(); i++ ) {
         // sepectrum
         Spectrum* spec = m_spectra->getSpectrum( i );
 
         // check
         if( spec->hasChromatogram() ) {
             const unsigned char stage = m_msFilters[ CLAMP( spec->getMsStage(), 1, 8 ) - 1 ];
             if( m_filter & stage ) {
                 spectra.push_back( spec );
             }
         }
     }
 }

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double kome::objects::SpectraChromatogram::getMinMz ( )

gets minimum value of m/z range

Returns: minimum value of m/z range (If m/z range doesn't have lower bound, this method returns negative number.)

Definition at line 102 of file SpectraChromatogram.cpp.

                                      {
     return m_minMz;
 }

double kome::objects::SpectraChromatogram::getMinRt ( )

gets minimum value of RT range

Returns: minimum value of RT range (If RT range doesn't have lower bound, this method returns negative number.)

Definition at line 134 of file SpectraChromatogram.cpp.

                                      {
     return m_minRt;
 }

bool kome::objects::SpectraChromatogram::isBPC ( )

judges whether chromatogram mode is BPC (Base Peak SpectraChromatogram)

Returns: whether chromatogram mode is BPC (Base Peak SpectraChromatogram)

Definition at line 180 of file SpectraChromatogram.cpp.

                                 {
     return !m_tic;
 }

bool kome::objects::SpectraChromatogram::isTIC ( )

judges whether chromatogram mode is TIC (Total Ion SpectraChromatogram)

Returns: whether chromatogram mode is TIC (Total Ion SpectraChromatogram)

Definition at line 175 of file SpectraChromatogram.cpp.

                                 {
     return m_tic;
 }

double kome::objects::SpectraChromatogram::onGetMass ( const unsigned int index )

protectedvirtual

This method is called by getMass method (override method)

Parameters

[in] index data index

Returns: mass

Implements kome::objects::Chromatogram.

Definition at line 367 of file SpectraChromatogram.cpp.

                                                                 {
     // get spectrum
     if( index >= m_spectra->getNumberOfSpectra() ) {
         return -1.0;
     }
     Spectrum* spec = m_spectra->getSpectrum( index );
     if( spec == NULL ) {
         return -1.0;
     }
 
     return spec->getBasePeakMass();
 }

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int kome::objects::SpectraChromatogram::onGetMsStage ( const unsigned int index )

protectedvirtual

This method is called by getMsStage method (override method)

Parameters

[in] index data index

Returns: MS stage.

Implements kome::objects::Chromatogram.

Definition at line 381 of file SpectraChromatogram.cpp.

                                                                 {
     // get spectrum
     if( index >= m_spectra->getNumberOfSpectra() ) {
         return -1;
     }
     Spectrum* spec = m_spectra->getSpectrum( index );
     if( spec == NULL ) {
         return -1;
     }
 
     return spec->getMsStage();
 }

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double kome::objects::SpectraChromatogram::onGetPrecursor ( const unsigned int index )

protectedvirtual

This method is called by getPrecursor method (override method)

Parameters

[in] index data index

Returns: precursor mass

Implements kome::objects::Chromatogram.

Definition at line 395 of file SpectraChromatogram.cpp.

                                                                      {
     // get spectrum
     if( index >= m_spectra->getNumberOfSpectra() ) {
         return -1.0;
     }
     Spectrum* spec = m_spectra->getSpectrum( index );
     if( spec == NULL ) {
         return -1.0;
     }
 
     return spec->getPrecursor();
 }

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void kome::objects::SpectraChromatogram::onGetSpectra	(	DataSet &	spectra,
		const double	startRt,
		const double	endRt,
		const SearchType	startSearch,
		const SearchType	endSearch
	)

protectedvirtual

This method is called by searchSpectrum or getDataSet method (overriede method)

Parameters

[out]	spectra	spectra object to store spectra
[in]	startRt	start RT
[in]	endRt	end RT
[in]	startSearch	start search type
[in]	endSearch	end search type

Implements kome::objects::Chromatogram.

Definition at line 345 of file SpectraChromatogram.cpp.

   {
     // get spectra
     std::vector< Spectrum* > specArray;
     getMemberSpectra( specArray );
 
     // search index
     int startIdx = std::max( 0, searchSpectrumIndex( specArray, startRt, startSearch ) );
     int endIdx = std::min( (int)specArray.size() - 1, searchSpectrumIndex( specArray, endRt, endSearch ) );
 
     // get spectra
     for( int i = startIdx; i <= endIdx; i++ ) {
         spectra.addSpectrum( specArray[ i ] );
     }
 }

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void kome::objects::SpectraChromatogram::onGetXYData ( kome::core::XYData *const xyData )

protectedvirtual

This method is called by getXYData method (override method)

Parameters

[out] xyData object to store data points

Implements kome::objects::Chromatogram.

Definition at line 290 of file SpectraChromatogram.cpp.

                                                                     {
     // get spectra
     std::vector< Spectrum* > spectra;
     std::set< Spectrum* > specSet;
     getMemberSpectra( spectra );
     for( unsigned int i = 0; i < spectra.size(); i++ ) {
         specSet.insert( spectra[ i ] );
     }
 
     // get xy data
     for( unsigned int i = 0; i < m_spectra->getNumberOfSpectra(); i++ ) {
         // spectrum
         Spectrum* spec = m_spectra->getSpectrum( i );
 
         // RT
         double rt = spec->getRt();
 
         // add point
         if( ( m_minRt < 0.0 || rt >= m_minRt ) && ( m_maxRt < 0.0 || rt <= m_maxRt )
                 && specSet.find( spec ) != specSet.end() ) {
             // intensity
             double intensity = 0.0;
 
             // @date 2012.10.03 <Mod> M.Izumi ->
             if( !m_proc ){
                 if( m_tic ) {
                     intensity = spec->getTotalIntensity( m_minMz, m_maxMz );
                 }
                 else {
                     intensity = spec->getMaxIntensity( m_minMz, m_maxMz );
                 }
             }else{ // Use data processing
                 kome::core::DataPoints dps;
                 spec->getXYData( &dps, true );
                 
                 for( unsigned int i=0; i < dps.getLength(); i++ ){
                     if( m_minMz < dps.getX(i) || dps.getX(i) >= m_maxMz ){
                         if( m_tic ){
                             intensity += dps.getY(i);   // TIC
                         }else{
                             intensity = std::max( intensity, dps.getY(i) ); // BPC
                         }
                     }
                 }
 
             }
             // @date 2012.10.03 <Mod> M.Izumi <-
             
             // add
             xyData->addPoint( rt, intensity );
         }
     }
 }

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int kome::objects::SpectraChromatogram::searchSpectrumIndex	(	std::vector< Spectrum * > &	spectra,
		const double	rt,
		SearchType	search
	)

protected

searches spectrum

Parameters

[in]	spectra	spectrum array
[in]	rt	retention time
[in]	search	search type

Returns: spectrum index

Definition at line 202 of file SpectraChromatogram.cpp.

                                                                                                                   {
     // search
     int idx = -1;
     double diff = 99999999999.9;
     for( int i = 0; i < (int)spectra.size(); i++ ) {
         // spectrum
         Spectrum* spec = spectra[ i ];
 
         // 
         if( search == SEARCH_PREV ) {
             if( spec->getRt() <= rt ) {
                 idx = i;
             }
         }
         else if( search == SEARCH_NEXT ) {
             if( spec->getRt() >= rt && idx < 0 ) {
                 idx = i;
             }
         }
         else {
             double d = fabs( spec->getRt() - rt );
             if( d < diff ) {
                 idx = i;
                 diff = d;
             }
         }
     }
 
     return idx;
 }

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void kome::objects::SpectraChromatogram::setFilter ( const unsigned char filter )

sets filter

Parameters

[in]

filter

The least significant bit is the ms1 filter.
The second least significant bit is the ms2 filter.
...
The most least significant bit is the ms8 or more filter.

Definition at line 144 of file SpectraChromatogram.cpp.

                                                                 {
     if( m_filter != filter ) {
         deleteXYData();
         m_filter = filter;
     }
 }

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void kome::objects::SpectraChromatogram::setMaxMz ( const double mz )

sets maximum value of m/z range

Parameters

[in] mz maximum value of m/z range (If mz is negative number, m/z range doesn't have upper bound.)

Definition at line 93 of file SpectraChromatogram.cpp.

                                                     {
     if( mz != m_maxMz ) {       
         deleteXYData();
         m_maxMz = mz;
     }
     setTitle();
 }

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void kome::objects::SpectraChromatogram::setMaxRt ( const double rt )

sets maximum value of RT range

Parameters

[in] rt maximum value of RT range (If maxRt is negative number, RT range doesn't have upper bound.)

Definition at line 126 of file SpectraChromatogram.cpp.

                                                     {
     if( rt != m_maxRt ) {
         deleteXYData();
         m_maxRt = rt;
     }
 }

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void kome::objects::SpectraChromatogram::setMinMz ( const double mz )

sets minimum value of m/z range

Parameters

[in] mz minimum value of m/z range (If mz is negative number, m/z range doesn't have lower bound.)

Definition at line 84 of file SpectraChromatogram.cpp.

                                                     {
     if( mz != m_minMz ) {
         deleteXYData();
         m_minMz = mz;
     }
     setTitle();
 }

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void kome::objects::SpectraChromatogram::setMinRt ( const double rt )

sets minimum value of RT range

Parameters

[in] rt minimum value of RT range (If minRt is negative number, RT range doesn't have lower bound.)

Definition at line 118 of file SpectraChromatogram.cpp.

                                                     {
     if( rt != m_minRt ) {
         deleteXYData();
         m_minRt = rt;
     }
 }

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void kome::objects::SpectraChromatogram::setMzRange	(	const double	minMz,
		const double	maxMz
	)

sets m/z range

Parameters

[in]	minMz	minimum value of m/z range (If minMz is negative number, m/z range doesn't have lower bound.)
[in]	maxMz	maximum value of m/z range (If minMz is negative number, m/z range doesn't have upper bound.)

Definition at line 78 of file SpectraChromatogram.cpp.

                                                                              {
     setMinMz( minMz );
     setMaxMz( maxMz );
 }

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void kome::objects::SpectraChromatogram::setRtRange	(	const double	minRt,
		const double	maxRt
	)

sets RT range

Parameters

[in]	minRt	minimum value of RT range (If minRt is negative number, RT range doesn't have lower bound.)
[in]	maxRt	maximum value of RT range (If maxRt is negative number, RT range doesn't have upper bound.)

Definition at line 112 of file SpectraChromatogram.cpp.

                                                                              {
     setMinRt( minRt );
     setMaxRt( maxRt );
 }

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Member Data Documentation

unsigned char kome::objects::SpectraChromatogram::m_filter

protected

filter

Definition at line 62 of file SpectraChromatogram.h.

double kome::objects::SpectraChromatogram::m_maxMz

protected

maximum value of m/z range

Definition at line 53 of file SpectraChromatogram.h.

double kome::objects::SpectraChromatogram::m_maxRt

protected

maximum value of RT range

Definition at line 59 of file SpectraChromatogram.h.

double kome::objects::SpectraChromatogram::m_minMz

protected

minimum value of m/z range

Definition at line 50 of file SpectraChromatogram.h.

double kome::objects::SpectraChromatogram::m_minRt

protected

minimum value of RT range

Definition at line 56 of file SpectraChromatogram.h.

const unsigned char SpectraChromatogram::m_msFilters

staticprotected

Initial value:

= {
    0x01,
    0x02,
    0x04,
    0x08,
    0x10,
    0x20,
    0x40,
    0x80
}

ms stage filter

Definition at line 71 of file SpectraChromatogram.h.

bool kome::objects::SpectraChromatogram::m_proc

protected

processed flg

Definition at line 68 of file SpectraChromatogram.h.

DataSet* kome::objects::SpectraChromatogram::m_spectra

protected

spectra

Definition at line 47 of file SpectraChromatogram.h.

bool kome::objects::SpectraChromatogram::m_tic

protected

TIC flag (true: TIC, false: BPC)

Definition at line 65 of file SpectraChromatogram.h.

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

DataObjects/SpectraChromatogram.h
DataObjects/SpectraChromatogram.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation