alignment class More...

#include <Alignment.h>

Inheritance diagram for kome::operation::Alignment:

Collaboration diagram for kome::operation::Alignment:

Public Member Functions
	Alignment ()
	constructor

virtual	~Alignment ()
	destructor

void	prepare (kome::objects::Sample standard, kome::objects::Sample treatment, kome::core::Progress *progress)
	prepares alignment More...

double	convertRt (const double rt, const double mz)
	gets aligned RT More...

double	convertMz (const double rt, const double mz)
	gets aligned m/z More...

double	invertRt (const double rt, const double mz)
	gets RT before alignment More...

double	invertMz (const double rt, const double mz)
	gets m/z before alignment More...

Static Public Member Functions
static Alignment &	getDefaultAlignment ()
	gets default alignment More...

Protected Member Functions
kome::objects::Sample *	getStandardSample ()
	gets the standard sample More...

kome::objects::Sample *	getTreatmentSample ()
	gets the treatment sample More...

virtual void	onPrepare (kome::objects::Sample standard, kome::objects::Sample treatment, kome::core::Progress *progress)=0
	This method is called by prepare method. (abstract method) More...

virtual double	onConvertRt (const double rt, const double mz)=0
	This method is called by convertRt method. (abstract method) More...

virtual double	onConvertMz (const double rt, const double mz)=0
	This method is called by convertMz method. (abstract method) More...

virtual double	onInvertRt (const double rt, const double mz)=0
	This method is called by invertRt method. (abstract method) More...

virtual double	onInvertMz (const double rt, const double mz)=0
	This method is called by invertMz method. (abstract method) More...

Protected Attributes
kome::objects::Sample *	m_standard

kome::objects::Sample *	m_treatment

Detailed Description

alignment class

Definition at line 26 of file Alignment.h.

Member Function Documentation

double kome::operation::Alignment::convertMz	(	const double	rt,
		const double	mz
	)

gets aligned m/z

Parameters

[in]	rt	RT before alignment
[in]	mz	m/z before alignment

Returns: aligned m/z

Definition at line 83 of file Alignment.cpp.

                                                               {
     // samples
     kome::objects::Sample* standard = getStandardSample();
     kome::objects::Sample* treatment = getTreatmentSample();
     if( standard == treatment || standard == NULL || treatment == NULL ) {
         return mz;
     }
 
     return onConvertMz( rt, mz );
 }

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double kome::operation::Alignment::convertRt	(	const double	rt,
		const double	mz
	)

gets aligned RT

Parameters

[in]	rt	RT before alignment
[in]	mz	m/z before alignment

Returns: aligned RT

Definition at line 71 of file Alignment.cpp.

                                                               {
     // samples
     kome::objects::Sample* standard = getStandardSample();
     kome::objects::Sample* treatment = getTreatmentSample();
     if( standard == treatment || standard == NULL || treatment == NULL ) {
         return rt;
     }
 
     return onConvertRt( rt, mz );
 }

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static Alignment & kome::operation::Alignment::getDefaultAlignment ( )

static

gets default alignment

Returns: default alignment

Definition at line 119 of file Alignment.cpp.

                                           {
     // create object
     static DefaultAlignment align;
 
     // remove from set
     AlignmentManager& mgr = AlignmentManager::getInstance();
     mgr.removeAlignment( &align );
 
     return align;
 }

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kome::objects::Sample * kome::operation::Alignment::getStandardSample ( )

protected

gets the standard sample

Returns: standard sample

Definition at line 46 of file Alignment.cpp.

                                                 {
     return m_standard;
 }

kome::objects::Sample * kome::operation::Alignment::getTreatmentSample ( )

protected

gets the treatment sample

Returns: treatment sample

Definition at line 51 of file Alignment.cpp.

                                                  {
     return m_treatment;
 }

double kome::operation::Alignment::invertMz	(	const double	rt,
		const double	mz
	)

gets m/z before alignment

Parameters

[in]	rt	aligned RT
[in]	mz	aligned m/z

Returns: m/z before alignemtn

Definition at line 107 of file Alignment.cpp.

                                                              {
     // samples
     kome::objects::Sample* standard = getStandardSample();
     kome::objects::Sample* treatment = getTreatmentSample();
     if( standard == treatment || standard == NULL || treatment == NULL ) {
         return mz;
     }
 
     return onInvertMz( rt, mz );
 }

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double kome::operation::Alignment::invertRt	(	const double	rt,
		const double	mz
	)

gets RT before alignment

Parameters

[in]	rt	aligned RT
[in]	mz	aligned m/z

Returns: RT before alignment

Definition at line 95 of file Alignment.cpp.

                                                              {
     // samples
     kome::objects::Sample* standard = getStandardSample();
     kome::objects::Sample* treatment = getTreatmentSample();
     if( standard == treatment || standard == NULL || treatment == NULL ) {
         return rt;
     }
 
     return onInvertRt( rt, mz );
 }

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double kome::operation::Alignment::onConvertMz	(	const double	rt,
		const double	mz
	)

protectedpure virtual

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

Parameters

[in]	rt	RT before alignment
[in]	mz	m/z before alignment

Returns: aligned m/z

Implemented in kome::operation::DefaultAlignment.

double kome::operation::Alignment::onConvertRt	(	const double	rt,
		const double	mz
	)

protectedpure virtual

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

Parameters

[in]	rt	RT before alignment
[in]	mz	m/z before alignment

Returns: aligned RT

Implemented in kome::operation::DefaultAlignment.

double kome::operation::Alignment::onInvertMz	(	const double	rt,
		const double	mz
	)

protectedpure virtual

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

Parameters

[in]	rt	aligned RT
[in]	mz	aligned m/z

Returns: m/z before alignemtn

Implemented in kome::operation::DefaultAlignment.

double kome::operation::Alignment::onInvertRt	(	const double	rt,
		const double	mz
	)

protectedpure virtual

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

Parameters

[in]	rt	aligned RT
[in]	mz	aligned m/z

Returns: RT before alignment

Implemented in kome::operation::DefaultAlignment.

void kome::operation::Alignment::onPrepare	(	kome::objects::Sample *	standard,
		kome::objects::Sample *	treatment,
		kome::core::Progress *	progress
	)

protectedpure virtual

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

Parameters

[in]	standard	standard sample
[in]	treatment	treatment sample
[in,out]	progress	the object to show the progress

Implemented in kome::operation::DefaultAlignment.

void kome::operation::Alignment::prepare	(	kome::objects::Sample *	standard,
		kome::objects::Sample *	treatment,
		kome::core::Progress *	progress
	)

prepares alignment

Parameters

[in]	standard	standard sample
[in]	treatment	treatment sample
[in,out]	progress	the object to show the progress

Definition at line 56 of file Alignment.cpp.

                                                                                                                {
     // set
     m_standard = standard;
     m_treatment = treatment;
 
     // progress
     if( progress == NULL ) {
         progress = &( kome::core::Progress::getIgnoringProgress() );
     }
 
     // prepare
     onPrepare( standard, treatment, progress );
 }

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Member Data Documentation

kome::objects::Sample* kome::operation::Alignment::m_standard

protected

standard sample

Definition at line 42 of file Alignment.h.

kome::objects::Sample* kome::operation::Alignment::m_treatment

protected

treatment sample

Definition at line 45 of file Alignment.h.

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

DataOperation/Alignment.h
DataOperation/Alignment.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

Member Data Documentation