averaged spectrum class More...

#include <AveragedSpectrum.h>

Inheritance diagram for kome::objects::AveragedSpectrum:

Collaboration diagram for kome::objects::AveragedSpectrum:

Public Member Functions
	AveragedSpectrum (DataGroupNode *group)
	constructor More...

virtual	~AveragedSpectrum ()
	destructor

void	addSpectrum (Spectrum *spectrum)
	add spectrum to array More...

unsigned int	getNumberOfSpectra ()
	gets the number of spectra More...

Spectrum *	getSpectrum (const unsigned int idx)
	gets spectrum More...

void	setMergeDistance (const double d)
	sets the merge disntace More...

double	getMergeDistance ()
	gets the merge distance More...

Public Member Functions inherited from kome::objects::Spectrum
	Spectrum (Sample sample, const char name)
	constructor More...

virtual	~Spectrum ()
	destructor

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

int	getId ()
	gets spectrum id More...

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

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

Sample *	getSample ()
	gets the sample that has this spectrum More...

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

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

void	setRt (const double rt)
	sets retention time More...

void	setRt (const double startRt, const double endRt)
	gets retention time More...

void	setStartRt (const double rt)
	sets start retention time More...

void	setEndRt (const double rt)
	sets end retention time More...

double	getRt ()
	gets retention time More...

double	getStartRt ()
	gets the start of retention time More...

double	getEndRt ()
	gets the end of retention time More...

void	setSpecType (const char *type)
	sets spectrum type More...

const char *	getSpecType ()
	gets spectrum type More...

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

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

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

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

void	getXYData (kome::core::XYData *const xyData, const double minX, const double maxX, const bool zero)
	gets data points that spectrum has More...

void	setXRange (const double minX, const double maxX)
	sets x range More...

void	setMinX (const double minX)
	sets min x More...

double	getMinX ()
	gets min x More...

void	setMaxX (const double maxX)
	sets max x More...

double	getMaxX ()
	gets max x More...

void	setTotalIntensity (const double intensity)
	sets total intensity of spectrum More...

double	getTotalIntensity (const double minX=-1.0, const double maxX=-1.0)
	gets total intensity in specified range More...

void	setMaxIntensity (const double intensity)
	sets max intensity of spectrum More...

double	getMaxIntensity (const double minX=-1.0, const double maxX=-1.0)
	gets max intensity in specified range More...

void	setBasePeakMass (const double mass)
	sets base peak mass More...

double	getBasePeakMass ()
	gets base peak mass More...

void	setMsStage (const int stage)
	sets ms stage More...

int	getMsStage ()
	gets ms stage More...

void	setPrecursor (const int stage, const double precursor)
	sets precursor More...

void	setPrecursor (const double precursor)
	sets precursor More...

double	getPrecursor (const int stage)
	gets precursor More...

double	getPrecursor ()
	gets the precursor mass of precursor ion spectrum. More...

void	setPrecursorIntensity (const int stage, const double intensity)
	sets precursor intensity More...

void	setPrecursorIntensity (const double intensity)
	sets precursor intensity More...

double	getPrecursorIntensity (const int stage)
	gets the precursor intensity More...

double	getPrecursorIntensity ()
	gets the precursor intensity of the precursor ion spectrum. More...

void	setPrecursorCharge (const int charge)
	sets the precursor charge More...

int	getPrecursorCharge ()
	gets the precursor charge More...

void	setParentSpectrum (Spectrum *const parent)
	sets parent spectrum More...

Spectrum *	getParentSpectrum ()
	gets parent spectrum More...

void	getChildSpectra (std::vector< Spectrum * > &children)
	gets child spectra More...

void	setHasChromatogram (const bool chromatogram)
	sets wheher this spectrum has chromatogram More...

bool	hasChromatogram ()
	judges whether this spectrum has chromatogram More...

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

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

void	setScanNumber (const int scan)
	sets scan number More...

int	getScanNumber ()
	gets scan number More...

void	setPolarity (Polarity polarity)
	sets polarity More...

Polarity	getPolarity ()
	gets polarity More...

void	setCentroidMode (const bool centroidMode)
	sets centroid mode or not More...

bool	isCentroidMode ()
	judget wheter this spectrum is centroid mode More...

void	setResolution (const double resolution)
	sets resolution More...

double	getResolution ()
	gets resolution More...

void	setCollisionEnergy (const char *collisionEnergy)
	sets the collision energy More...

const char *	getCollisionEnergy ()
	gets the collision energy More...

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

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

void	setAutoZeroPoints (const bool autoZero)
	sets auto zero points flag value More...

bool	isAutoZeroPoints ()
	gets auto zero points flag value More...

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

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

void	setOrgSpectrum (Spectrum *spec)
	sets original spectrum More...

Spectrum *	getOrgSpectrum ()
	gets original spectrum More...

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

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

void	setSpotId (const char *pcSpotId)
	set spot id param[in] pcSpotId SpotId information

const char *	getSpotId (void)
	get spot id More...

void	setRequestLoadData (void)
	set the flag of request load data More...

void	resetRequestLoadData (void)

bool	isRequestLoadData (void)
	check the flag of request load data More...

void	setFirstAccess (void)
	set the flag of first access

void	resetFirstAccess (void)
	reset the flag of first access

bool	isFirstAccess (void)
	check the flag of first access More...

bool	loadData (void)
	load data More...

Static Public Member Functions
static void	getAveragedDataPoints (kome::objects::Spectrum **spectra, const unsigned int num, kome::core::XYData &xyData)
	gets the averaged data points More...

static void	mergeDataPoints (kome::core::XYData &src0, kome::core::XYData &src1, kome::core::XYData &dst)
	merges data points More...

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

Protected Member Functions
void	updateTitle ()
	update title

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

virtual void	onGetXRange (double minX, double maxX)
	This method is called by getMinX or getMaxX method. (override method) More...

virtual double	onGetTotalIntensity (const double minX, const double maxX)
	This method is called by getTotalIntensity method. (override method) More...

virtual double	onGetMaxIntensity (const double minX, const double maxX)
	This method is called by getMaxIntensity method. (override method) More...

Protected Member Functions inherited from kome::objects::Spectrum
virtual void	onSetRequestLoadData (void)
	This method is called by setRequestLoadData method. (abstract method)

virtual void	onResetRequestLoadData (void)
	This method is called by resetRequestLoadData method. (abstract method)

virtual bool	onIsRequestLoadData (void)
	This method is called by isRequestLoadData method. (abstract method) More...

virtual void	onSetFirstAccess (void)
	This method is called by setFirstAccess method. (abstract method)

virtual void	onResetFirstAccess (void)
	This method is called by resetFirstAccess method. (abstract method)

virtual bool	onIsFirstAccess (void)
	This method is called by isFirstAccess method. (abstract method) More...

virtual bool	onLoadData (void)
	This method is called by loadData method. (abstract method) More...

bool	firstAccessProcess (void)
	method for processing when accessing the first item of this class More...

Protected Attributes
std::vector< Spectrum * >	m_spectra

double	m_d

Protected Attributes inherited from kome::objects::Spectrum
Spectrum *	m_orgSpec

bool	m_op

int	m_specId

Additional Inherited Members
Public Types inherited from kome::objects::Spectrum
enum	Polarity { POLARITY_UNKNOWN = 0, POLARITY_POSITIVE = 1, POLARITY_NEGATIVE = 2 }
	polarity definition

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

Detailed Description

averaged spectrum class

Definition at line 29 of file AveragedSpectrum.h.

Constructor & Destructor Documentation

kome::objects::AveragedSpectrum::AveragedSpectrum ( DataGroupNode * group )

constructor

Parameters

[in] group spectrum group object that has this spectrum

Definition at line 35 of file AveragedSpectrum.cpp.

         : Spectrum( ( group == NULL ? NULL : group->getSample() ), "" ) {
     m_d = 0.05;
     setGroup( group );
 }

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Member Function Documentation

void kome::objects::AveragedSpectrum::addSpectrum ( Spectrum * spectrum )

add spectrum to array

Parameters

[in] spectrum spectrum object to be added

Definition at line 46 of file AveragedSpectrum.cpp.

                                                        {
     // update stage
     if( m_spectra.size() == 0 ) {
         setMsStage( spectrum->getMsStage() );
     }
     else if( spectrum->getMsStage() != getMsStage() ) {
         setMsStage( -1 );
     }
 
     // update RT
     double startRt = getStartRt();
     if( spectrum->getStartRt() >= 0.0
             && ( spectrum->getStartRt() < startRt || startRt < 0.0 ) ) {
         setStartRt( spectrum->getStartRt() );
     }
     double endRt = getEndRt();
     if( spectrum->getEndRt() >= 0.0
             && ( spectrum->getEndRt() > endRt || endRt < 0.0 ) ) {
         setEndRt( spectrum->getEndRt() );
     }
 
     // TIC, BPC, BPI
     if( m_spectra.size() == 0 ) {
         setTotalIntensity( spectrum->getTotalIntensity() );
         setMaxIntensity( spectrum->getMaxIntensity() );
         setBasePeakMass( spectrum->getBasePeakMass() );
     }
     else {
         // TIC
         double tic = getTotalIntensity() * (double)m_spectra.size();
         tic += spectrum->getTotalIntensity();
         tic /= (double)( m_spectra.size() + 1 );
         setTotalIntensity( tic );
 
         // BPC, BPI
         if( spectrum->getMaxIntensity() > getMaxIntensity() ) {
             setMaxIntensity( spectrum->getMaxIntensity() );
             setBasePeakMass( spectrum->getBasePeakMass() );
         }
     }
 
     // precursor
     double precursor = 0.0;
     int precCnt = 0;
     for( unsigned int i = 0; i < m_spectra.size(); i++ ) {
         double tmpPrec = m_spectra[ i ]->getPrecursor();
         if( tmpPrec > 0.0 ) {
             precursor += tmpPrec;
             precCnt++;
         }
     }
     if( precCnt > 0 ) {
         precursor /= (double)precCnt;
         setPrecursor( precursor );
     }
 
     // add spectrum to array
     m_spectra.push_back( spectrum );
 
     // update title @date 2011.02.07 <Add> M.Izumi
     updateTitle();
 }

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static void kome::objects::AveragedSpectrum::getAveragedDataPoints	(	kome::objects::Spectrum **	spectra,
		const unsigned int	num,
		kome::core::XYData &	xyData
	)

static

gets the averaged data points

Parameters

[in]	spectra	the array of spectra
[in]	num	the spectrum array size
[out]	xyData	the object to store data points.

Definition at line 234 of file AveragedSpectrum.cpp.

                                                                                                                             {
     // check parameters
     if( spectra == NULL || num == 0 ) {
         return;
     }
 
     // get data points
     if( num == 1 ) {
         spectra[ 0 ]->getXYData( &xyData, -1.0, -1.0, false );
     }
     else {
         unsigned int mid = num / 2;
 
         kome::core::DataPoints dps0;
         getAveragedDataPoints( spectra, mid, dps0 );
 
         kome::core::DataPoints dps1;
         getAveragedDataPoints( spectra + mid, num - mid, dps1 );
 
         mergeDataPoints( dps0, dps1, xyData );
     }
 }

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double kome::objects::AveragedSpectrum::getMergeDistance ( )

gets the merge distance

Returns: merge distance

Definition at line 128 of file AveragedSpectrum.cpp.

                                           {
     return m_d;
 }

unsigned int kome::objects::AveragedSpectrum::getNumberOfSpectra ( )

gets the number of spectra

Returns: the number of spectra

Definition at line 110 of file AveragedSpectrum.cpp.

                                                   {
     return m_spectra.size();
 }

Spectrum * kome::objects::AveragedSpectrum::getSpectrum ( const unsigned int idx )

gets spectrum

Parameters

[in] idx spectrum index

Returns: spectrum (If NULL, the index is illegal.)

Definition at line 115 of file AveragedSpectrum.cpp.

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

static void kome::objects::AveragedSpectrum::mergeDataPoints	(	kome::core::XYData &	src0,
		kome::core::XYData &	src1,
		kome::core::XYData &	dst
	)

static

merges data points

Parameters

[in]	src0	source data points
[in]	src1	source data points
[out]	dst	the object to store merged data points

Definition at line 258 of file AveragedSpectrum.cpp.

                                                                                                         {
     // points
     class Point {
     public:
         Point() {};
         virtual ~Point() {};
     public:
         double x;
         double y;
         int spec;
     public:
         static bool lessPoint( Point& p0, Point& p1 ) {
             return ( p0.x < p1.x );
         };
     };
     std::vector< Point > points;
 
     double d = 0.05;
     double prevX = -1.0;
 
     // first data points
     const unsigned int len0 = src0.getLength();
     for( unsigned int i = 0; i < len0; i++ ) {
         const double x = src0.getX( i );
         const double y = src0.getY( i );
         if( y > 0.0 ) {
             points.resize( points.size() + 1 );
             points.back().x = x;
             points.back().y = y;
             points.back().spec = 0;
 
             if( prevX > 0.0 ) {
                 double tmpD = fabs( x - prevX );
                 if( tmpD < d ) {
                     d = tmpD;
                 }
             }
             prevX = x;
         }
     }
 
     // second data points
     const unsigned int len1 = src1.getLength();
     for( unsigned int i = 0; i < len1; i++ ) {
         const double x = src1.getX( i );
         const double y = src1.getY( i );
         if( y > 0.0 ) {
             points.resize( points.size() + 1 );
             points.back().x = x;
             points.back().y = y;
             points.back().spec = 1;
 
             if( prevX > 0.0 ) {
                 double tmpD = fabs( x - prevX );
                 if( tmpD < d ) {
                     d = tmpD;
                 }
             }
             prevX = x;
         }
     }
 
     // sort
     std::sort( points.begin(), points.end(), Point::lessPoint );
 
     // add point
     std::set< int > specSet;
     double sumX = 0.0;
     double sumY = 0.0;
     for( unsigned int i = 0; i < points.size(); i++ ) {
         const double x = points[ i ].x;
         const double y = points[ i ].y;
         const int spec = points[ i ].spec;
 
         if( !specSet.empty() ) {
             double tmpX = sumX / sumY;
             if( specSet.find( spec ) != specSet.end() || tmpX + d < x ) {
                 double tmpY = sumY;
                 dst.addPoint( tmpX, tmpY );
                 specSet.clear();
             }
         }
 
         if( specSet.empty() ) {
             sumX = x * y;
             sumY = y;
         }
         else {
             sumX = sumX + x * y;
             sumY = sumY + y;
         }
 
         specSet.insert( spec );
     }
 
     if( !specSet.empty() ) {
         double tmpX = sumX / sumY;
         double tmpY = sumY;
         dst.addPoint( tmpX, tmpY );
     }
 }

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double kome::objects::AveragedSpectrum::onGetMaxIntensity	(	const double	minX,
		const double	maxX
	)

protectedvirtual

This method is called by getMaxIntensity method. (override method)

Parameters

[in]	minX	minimum x of range (If minX is negative number, minimum x value is unbounded.)
[in]	maxX	maximum x of range (If maxX is negative number, maximum x value is unbounded.)

Returns: max intensity

Implements kome::objects::Spectrum.

Definition at line 220 of file AveragedSpectrum.cpp.

                                                                                  {
     // get max intensity
     double intensity = 0.0;
     for( unsigned int i = 0; i < m_spectra.size(); i++ ) {
         double y = m_spectra[ i ]->getMaxIntensity( minX, maxX );
         if( y > intensity ) {
             intensity = y;
         }
     }
 
     return intensity;
 }

double kome::objects::AveragedSpectrum::onGetTotalIntensity	(	const double	minX,
		const double	maxX
	)

protectedvirtual

This method is called by getTotalIntensity method. (override method)

Parameters

[in]	minX	minimum x of range (If minX is negative number, minimum x value is unbounded.)
[in]	maxX	maximum x of range (If maxX is negative number, maximum x value is unbounded.)

Returns: total intensity

Implements kome::objects::Spectrum.

Definition at line 208 of file AveragedSpectrum.cpp.

                                                                                    {
     // get total intensity
     double intensity = 0.0;
     for( unsigned int i = 0; i < m_spectra.size(); i++ ) {
         intensity += m_spectra[ i ]->getTotalIntensity( minX, maxX );
     }
     intensity /= (double)m_spectra.size();
 
     return intensity;
 }

void kome::objects::AveragedSpectrum::onGetXRange	(	double *	minX,
		double *	maxX
	)

protectedvirtual

This method is called by getMinX or getMaxX method. (override method)

Parameters

[out]	minX	the pointer to store minimum x value
[out]	maxX	the pointer to store maximum x value

Implements kome::objects::Spectrum.

Definition at line 184 of file AveragedSpectrum.cpp.

                                                                {
     double minXX = double();
     double maxXX = double();
 
     // get x range
     if( m_spectra.size() > 0 ) {
         minXX = m_spectra[ 0 ]->getMinX();      
         maxXX = m_spectra[ 0 ]->getMaxX();
 
         for( unsigned int i = 1; i < m_spectra.size(); i++ ) {
             double tmpMinX = m_spectra[ i ]->getMinX();
             double tmpMaxX = m_spectra[ i ]->getMaxX();
 
             minXX = MIN( minXX, tmpMinX );
             maxXX = MAX( maxXX, tmpMaxX );
         }
     }
 
     // store
     *minX = minXX;
     *maxX = maxXX;
 }

void kome::objects::AveragedSpectrum::onGetXYData	(	kome::core::XYData *const	xyData,
		const double	minX,
		const double	maxX
	)

protectedvirtual

This method is called by getXYData method. (override method)

Parameters

[out]	xyData	the object to store data points
[in]	minX	minimum x value. (If minX is negative number, minimum x value is not unbounded.)
[in]	maxX	maximum x value. (If maxX is negative number, maximum x value is not unbounded.)

Implements kome::objects::Spectrum.

Definition at line 147 of file AveragedSpectrum.cpp.

   {
     // check spectra
     if( m_spectra.size() == 0 ) {
         return;
     }
 
     bool isProfile = false;;
     for( unsigned int i = 0; i < m_spectra.size() && !isProfile; i++ ) {
         if( !m_spectra[ i ]->isCentroidMode() ) {
             isProfile = true;
         }
     }
 
     setCentroidMode( !isProfile );
 
 
     // data points
     kome::core::DataPoints dps;
     if( m_spectra.size() > 0 ) {
         getAveragedDataPoints( &( m_spectra[ 0 ] ), m_spectra.size(), dps );
 
         for( unsigned int i = 0; i < dps.getLength(); i++ ) {
             const double x = dps.getX( i );
             const double y = dps.getY( i ) / (double)m_spectra.size();
 
             if( ( minX < 0.0 || x >= minX ) && ( maxX < 0.0 || x <= maxX ) ) {
                 xyData->addPoint( x, y );
             }
         }
     }
 }

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void kome::objects::AveragedSpectrum::setMergeDistance ( const double d )

sets the merge disntace

Parameters

[in] d merge disntance

Definition at line 123 of file AveragedSpectrum.cpp.

                                                         {
     m_d = std::max( d, 0.0 );
 }

Member Data Documentation

double kome::objects::AveragedSpectrum::m_d

protected

merge distance

Definition at line 49 of file AveragedSpectrum.h.

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

protected

the array of spectra

Definition at line 46 of file AveragedSpectrum.h.

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

DataObjects/AveragedSpectrum.h
DataObjects/AveragedSpectrum.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation