kome::operation::ManipulatedSpectrum Class Reference

ManipulatedSpectrum class. More...

#include <ManipulatedSpectrum.h>

Inheritance diagram for kome::operation::ManipulatedSpectrum:

Collaboration diagram for kome::operation::ManipulatedSpectrum:

Public Member Functions
	ManipulatedSpectrum (ManipulatedSample *sample, kome::objects::Spectrum &org, const bool op=false)
	constructor More...
virtual	~ManipulatedSpectrum ()
	destructor
void	setSample (ManipulatedSample *sample)
	set sample object More...
ManipulatedSample *	getSample ()
	get sample object 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...

Protected Member Functions
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...
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...
Protected Member Functions inherited from kome::objects::Spectrum
bool	firstAccessProcess (void)
	method for processing when accessing the first item of this class More...

Protected Attributes
kome::objects::Spectrum &	m_org
ManipulatedSample *	m_sample
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 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...
Static Protected Attributes inherited from kome::objects::Spectrum
static std::vector< std::string >	m_commonProps

Detailed Description

ManipulatedSpectrum class.

Definition at line 22 of file ManipulatedSpectrum.h.

Constructor & Destructor Documentation

kome::operation::ManipulatedSpectrum::ManipulatedSpectrum	(	ManipulatedSample *	sample,
		kome::objects::Spectrum &	org,
		const bool	op = false
	)

constructor

Parameters

sample
org
op

Definition at line 26 of file ManipulatedSpectrum.cpp.

    : kome::objects::Spectrum( org.getSample(), org.getName() ), m_org( org ){
    m_op = op;
    
    setName( org.getName() );
    setRt( org.getRt() );
    setStartRt( org.getStartRt() );
    setEndRt( org.getEndRt() );
    setSpecType( org.getSpecType() );
    setTitle( org.getTitle() );
    setIcon( org.getIcon() );
    setMinX( org.getMinX() );
    setMaxX( org.getMaxX() );
    setTotalIntensity( org.getTotalIntensity() );
    setBasePeakMass( org.getBasePeakMass() );
    setMsStage( org.getMsStage() );
    setPrecursor( org.getPrecursor() );
    setPrecursorIntensity( org.getPrecursorIntensity() );
    setParentSpectrum( org.getParentSpectrum() );
    setHasChromatogram( org.hasChromatogram() );
    setGroup( org.getGroup() );
    setScanNumber( org.getScanNumber() );
    setPolarity( org.getPolarity() );
    setCentroidMode( org.isCentroidMode() );
    setResolution( org.getResolution() );
    setOrgSpectrum( org.getOrgSpectrum() );

    m_sample = sample;
}

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Member Function Documentation

ManipulatedSample * kome::operation::ManipulatedSpectrum::getSample ( )

inline

get sample object

Returns

sample

Definition at line 60 of file ManipulatedSpectrum.h.

{ return m_sample; }

double kome::operation::ManipulatedSpectrum::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 128 of file ManipulatedSpectrum.cpp.

                                                                                   {
    // get data points
    kome::core::DataPoints pt;
    onGetXYData( &pt, minX, maxX );

    // get main intensity
    double intensity = 0.0;
    for( unsigned int i = 0; i < pt.getLength(); i++ ) {
        double y = pt.getY( i );
        intensity = MAX( y, intensity );
    }

    return intensity;
}

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double kome::operation::ManipulatedSpectrum::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 113 of file ManipulatedSpectrum.cpp.

                                                                                     {
        // get data points
    kome::core::DataPoints pt;
    onGetXYData( &pt, minX, maxX );

    // get total intensity
    double intensity = 0.0;
    for( unsigned int i = 0; i < pt.getLength(); i++ ) {
        intensity += pt.getY( i );
    }

    return intensity;
}

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void kome::operation::ManipulatedSpectrum::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 109 of file ManipulatedSpectrum.cpp.

                                                                 {
}

void kome::operation::ManipulatedSpectrum::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 61 of file ManipulatedSpectrum.cpp.

 {
    // manipulate
    ManipulatedSample* sample = getSample();

    // operaiton list
    std::vector< kome::objects::XYDataOperation* > operations;
    if( sample != NULL ) {
        for( unsigned int i = 0; i < sample->getNumberOfOperation(); i++ ) {
            operations.push_back( sample->getOperation( i ) );
        }
    }

    // points
    if( operations.size() == 0 ) {
        m_org.getXYData( xyData, minX, maxX, false );
    }
    else {
        kome::core::DataPoints dps;
        m_org.getXYData( &dps, -1.0, -1.0, false );

        for( unsigned int i = 0; i < operations.size(); i++ ) {
            kome::objects::XYDataOperation* opt = operations[ i ];

            kome::core::DataPoints tmp;
            opt->update( dps, tmp, *this );

            dps.clearPoints();
            for( unsigned int i = 0; i < tmp.getLength(); i++ ) {
                dps.addPoint( tmp.getX( i ), tmp.getY( i ) );
            }
        }

        // copy
        for( unsigned int i = 0; i < dps.getLength(); i++ ) {
            const double x = dps.getX( i );
            const double y = dps.getY( i );
            if( ( minX < 0.0 || x >= minX ) && ( maxX < 0.0 || x <= maxX ) ) {
                xyData->addPoint( x, y );
            }
        }
    }
}

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bool kome::operation::ManipulatedSpectrum::onIsFirstAccess ( void  )

protectedvirtual

This method is called by isFirstAccess method. (abstract method)

Returns

If true, the first accessing.

Reimplemented from kome::objects::Spectrum.

Definition at line 176 of file ManipulatedSpectrum.cpp.

{
    return  kome::objects::Spectrum::onIsFirstAccess( );
}

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bool kome::operation::ManipulatedSpectrum::onIsRequestLoadData ( void  )

protectedvirtual

This method is called by isRequestLoadData method. (abstract method)

Returns

If true, file read request is valid.

Reimplemented from kome::objects::Spectrum.

Definition at line 158 of file ManipulatedSpectrum.cpp.

{
    return  kome::objects::Spectrum::onIsRequestLoadData( );
}

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bool kome::operation::ManipulatedSpectrum::onLoadData ( void  )

protectedvirtual

This method is called by loadData method. (abstract method)

Returns

If true, file reading success.

Reimplemented from kome::objects::Spectrum.

Definition at line 182 of file ManipulatedSpectrum.cpp.

{
    return  kome::objects::Spectrum::onLoadData( );
}

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void kome::operation::ManipulatedSpectrum::setSample ( ManipulatedSample *  sample )

inline

set sample object

Parameters

sample

Definition at line 53 of file ManipulatedSpectrum.h.

{ m_sample = sample; }

Member Data Documentation

kome::objects::Spectrum& kome::operation::ManipulatedSpectrum::m_org

protected

original spectrum

Definition at line 41 of file ManipulatedSpectrum.h.

ManipulatedSample* kome::operation::ManipulatedSpectrum::m_sample

protected

sample object

Definition at line 45 of file ManipulatedSpectrum.h.

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

• DataOperation/ManipulatedSpectrum.h
• DataOperation/ManipulatedSpectrum.cpp