aligned chromatogram class More...

#include <AlignedChromatogram.h>

Inheritance diagram for kome::operation::AlignedChromatogram:

Collaboration diagram for kome::operation::AlignedChromatogram:

Public Member Functions
	AlignedChromatogram (kome::objects::Chromatogram &org, Alignment *align)
	constructor More...

virtual	~AlignedChromatogram ()
	destructor

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

virtual void	onGetSpectra (kome::objects::DataSet &spectra, const double startRt, const double endRt, const kome::objects::SearchType startSearch, const kome::objects::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
kome::objects::Chromatogram &	m_org

Alignment *	m_align

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

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...

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

Detailed Description

aligned chromatogram class

Definition at line 26 of file AlignedChromatogram.h.

Constructor & Destructor Documentation

kome::operation::AlignedChromatogram::AlignedChromatogram	(	kome::objects::Chromatogram &	org,
		Alignment *	align
	)

constructor

Parameters

[in]	org	original chromatogram
[in]	align	alignment

Definition at line 28 of file AlignedChromatogram.cpp.

         : kome::objects::Chromatogram( org.getSample() ), m_org( org ) {
     // initialize
     m_align = align;
     if( m_align == NULL ) {
         m_align = &( Alignment::getDefaultAlignment() );
     }
 
     setOrgChromatogram( org.getOrgChromatogram() );
 }

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Member Function Documentation

double kome::operation::AlignedChromatogram::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 97 of file AlignedChromatogram.cpp.

                                                                 {
     return m_org.getMass( index );
 }

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int kome::operation::AlignedChromatogram::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 102 of file AlignedChromatogram.cpp.

                                                                 {
     return m_org.getMsStage( index );
 }

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double kome::operation::AlignedChromatogram::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 107 of file AlignedChromatogram.cpp.

                                                                      {
     return m_org.getPrecursor( index );
 }

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void kome::operation::AlignedChromatogram::onGetSpectra	(	kome::objects::DataSet &	spectra,
		const double	startRt,
		const double	endRt,
		const kome::objects::SearchType	startSearch,
		const kome::objects::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 64 of file AlignedChromatogram.cpp.

   {
     // get xy data
     kome::core::DataPoints dps0;
     kome::core::DataPoints dps1;
     kome::core::DataPoints dps2;
 
     m_org.getXYData( &dps0, false );
     onGetXYData( &dps1 );
 
     // add aligned xy data
     if( dps0.getLength() > 0 ) {
         dps2.reserve( dps0.getLength() );
     }
 
     for( unsigned int i = 0; i < dps0.getLength(); i++ ) {
         dps2.addPoint( dps1.getX( 0 ), dps0.getX( i ) );
     }
 
     // get org RT
     const double orgStartRt = kome::numeric::Interpolation::linear( dps2, startRt );
     const double orgEndRt = kome::numeric::Interpolation::linear( dps2, endRt );
 
     // get spectra
     m_org.getSpectra( spectra, orgStartRt, orgEndRt, startSearch, endSearch );
 }

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void kome::operation::AlignedChromatogram::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 44 of file AlignedChromatogram.cpp.

                                                                     {
     // check the parameter
     if( xyData == NULL ) {
         return;
     }
 
     // get xy data
     kome::core::DataPoints dps;
     m_org.getXYData( &dps, false );
 
     // add points
     for( unsigned int i = 0; i < dps.getLength(); i++ ) {
         const double x = m_align->convertRt( dps.getX( i ), m_org.getMz() );
         const double y = dps.getY( i );
 
         xyData->addPoint( x, y );
     }
 }

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Member Data Documentation

Alignment* kome::operation::AlignedChromatogram::m_align

protected

alignment

Definition at line 47 of file AlignedChromatogram.h.

kome::objects::Chromatogram& kome::operation::AlignedChromatogram::m_org

protected

original chromatogram

Definition at line 44 of file AlignedChromatogram.h.

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

DataOperation/AlignedChromatogram.h
DataOperation/AlignedChromatogram.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation