peaks management class More...

#include <PeaksManager.h>

Inheritance diagram for kome::objects::PeaksManager:

Collaboration diagram for kome::objects::PeaksManager:

Public Member Functions
Peaks *	getPeaks (Spectrum *spec)
	gets peaks of specified spectrum More...

Peaks *	getPeaks (Chromatogram *chrom)
	gets peaks of specified chromatogram More...

Peaks2D *	getPeaks (DataGroupNode *group)
	gets peak of specified spectrum group More...

Peaks *	createPeaks (Spectrum *spec)
	creates peaks of specified spectrum More...

Peaks *	createPeaks (Chromatogram *chrom)
	creates peaks of specified chromatogram More...

Peaks2D *	createPeaks (DataGroupNode *group)
	creates peaks of specified spectrum group More...

bool	hasPeaks (Spectrum *spec)
	judges whether peaks object of specified spectrum exists More...

bool	hasPeaks (Chromatogram *chrom)
	judges whether peaks object of specified chromatogram exists More...

bool	hasPeaks (DataGroupNode *group)
	judges whether peaks object of specified spectrum group exists More...

void	deletePeaks (Spectrum *spec)
	deletes peaks of specified spectrum More...

void	deletePeaks (Chromatogram *chrom)
	deletes peaks of specified chromatogram More...

void	deletePeaks (DataGroupNode *group)
	deletes peaks of specified spectrum group More...

void	updatePeaks (Spectrum &spec, Peaks *peaks, std::vector< PeakElement > &addPeaks)
	update peaks More...

Static Public Member Functions
static PeaksManager &	getInstance ()
	get peaks manager object (This is the only object.) More...

Static Public Member Functions inherited from kome::objects::DataManager
static void	openSample (Sample *sample)
	This method is called when a sample is opened. More...

static void	closeSample (Sample *sample, const bool deleting)
	This method is called when a sample is closed. More...

static void	openSpectrum (Spectrum *spec)
	This method is called when a spectrum is opened. More...

static void	closeSpectrum (Spectrum *spec, const bool deleting)
	This method is called when a spectrum is closed. More...

static void	openChromatogram (Chromatogram *chrom)
	This method is called when a chromaogram is opened. More...

static void	closeChromatogram (Chromatogram *chrom, const bool deleting)
	This method is called when a chromatogram is closed. More...

static void	openDataMap (DataMapInfo *dataMap)
	This method is called when a data map is opened. More...

static void	closeDataMap (DataMapInfo *dataMap, const bool deleting)
	This method is called when a data map is closed. More...

Protected Member Functions
	PeaksManager ()
	constructor

virtual	~PeaksManager ()
	destructor

virtual void	onCloseSample (Sample *sample, const bool deleting)
	This method is called when a sample is closed. (override method) More...

Protected Member Functions inherited from kome::objects::DefaultDataManager
	DefaultDataManager ()
	constructor

virtual	~DefaultDataManager ()
	destructor

virtual void	onOpenSample (Sample *sample)
	This method is called when a sample is opened. (override method) More...

virtual void	onOpenSpectrum (Spectrum *spec)
	This method is called when a spectrum is opened. (override method) More...

virtual void	onCloseSpectrum (Spectrum *spec, const bool deleting)
	This method is called when a spectrum is closed. (override method) More...

virtual void	onOpenChromatogram (Chromatogram *chrom)
	This method is called when a chromatogram is opened. (override method) More...

virtual void	onCloseChromatogram (Chromatogram *chrom, const bool deleting)
	This method is called when a chromatogram is closed. (override method) More...

virtual void	onOpenDataMap (DataMapInfo *dataMap)
	This method is called when a data map is opened. (override method) More...

virtual void	onCloseDataMap (DataMapInfo *dataMap, const bool deleting)
	This method is called when a data map is closed. (override method) More...

Protected Member Functions inherited from kome::objects::DataManager
	DataManager ()
	constructor

virtual	~DataManager ()
	destructor

Protected Attributes
std::map< Spectrum *, Peaks >	m_specPeaksMap

std::map< Chromatogram *, Peaks >	m_chromPeaksMap

std::map< DataGroupNode *, Peaks2D >	m_2dPeaksMap

Protected Attributes inherited from kome::objects::DataManager
int	m_order

Additional Inherited Members
Static Protected Member Functions inherited from kome::objects::DataManager
static bool	lessManager (DataManager dm0, DataManager dm1)
	conmapred data managers to sort More...

static void	sortDataManagers ()
	sorts data managers

Static Protected Attributes inherited from kome::objects::DataManager
static std::vector< DataManager * >	m_dataMgrs

static bool	m_sorted = true

Detailed Description

peaks management class

Definition at line 41 of file PeaksManager.h.

Member Function Documentation

Peaks * kome::objects::PeaksManager::createPeaks ( Spectrum * spec )

creates peaks of specified spectrum

Parameters

[in] spec spectrum

Returns: peaks object

Definition at line 85 of file PeaksManager.cpp.

                                                  {
     // check the parameter
     if( spec == NULL ) {
         return NULL;
     }
 
     // create peaks
     Peaks* peaks = getPeaks( spec );
     if( peaks == NULL ) {
         peaks = &( m_specPeaksMap[ spec ] );
     }
     else {
         peaks->clearPoints();
     }
 
     // set precursor
     peaks->setPrecursor( spec->getPrecursor() );
 
     return peaks;
 }

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Peaks * kome::objects::PeaksManager::createPeaks ( Chromatogram * chrom )

creates peaks of specified chromatogram

Parameters

[in] chrom chromatogram

Returns: peaks object

Definition at line 107 of file PeaksManager.cpp.

                                                       {
     // check the parameter
     if( chrom == NULL ) {
         return NULL;
     }
 
     // create peaks
     Peaks* peaks = getPeaks( chrom );
     if( peaks == NULL ) {
         peaks = &( m_chromPeaksMap[ chrom ] );
     }
     else {
         peaks->clearPoints();
     }
 
     return peaks;
 }

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Peaks2D * kome::objects::PeaksManager::createPeaks ( DataGroupNode * group )

creates peaks of specified spectrum group

Parameters

[in] group spectrum group

Returns: peak object

Definition at line 126 of file PeaksManager.cpp.

                                                          {
     // check the parameter
     if( group == NULL ) {
         return NULL;
     }
 
     // create peaks
     Peaks2D* peaks = getPeaks( group );
     if( peaks == NULL ) {
         peaks = &( m_2dPeaksMap[ group ] );
     }
     else {
         peaks->clearClusters();
         peaks->clearPeaks();
     }
 
     return peaks;
 }

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void kome::objects::PeaksManager::deletePeaks ( Spectrum * spec )

deletes peaks of specified spectrum

Parameters

[in] spec spectrum

Definition at line 161 of file PeaksManager.cpp.

                                                {
     if( m_specPeaksMap.find( spec ) != m_specPeaksMap.end() ) {
         m_specPeaksMap.erase( spec );
     }
 }

void kome::objects::PeaksManager::deletePeaks ( Chromatogram * chrom )

deletes peaks of specified chromatogram

Parameters

[in] chrom chromatogram

Definition at line 168 of file PeaksManager.cpp.

                                                     {
     if( m_chromPeaksMap.find( chrom ) != m_chromPeaksMap.end() ) {
         m_chromPeaksMap.erase( chrom );
     }
 }

void kome::objects::PeaksManager::deletePeaks ( DataGroupNode * group )

deletes peaks of specified spectrum group

Parameters

[in] group spectrum group

Definition at line 175 of file PeaksManager.cpp.

                                                      {
     if( m_2dPeaksMap.find( group ) != m_2dPeaksMap.end() ) {
         m_2dPeaksMap.erase( group );
     }
 }

static PeaksManager & kome::objects::PeaksManager::getInstance ( )

static

get peaks manager object (This is the only object.)

Returns: peaks manager object

Definition at line 263 of file PeaksManager.cpp.

                                         {
     // create object (This is the only object.)
     static PeaksManager mgr;
 
     return mgr;
 }

Peaks * kome::objects::PeaksManager::getPeaks ( Spectrum * spec )

gets peaks of specified spectrum

Parameters

[in] spec spectrum

Returns: peaks object (If NULL, peaks object is not created yet.)

Definition at line 43 of file PeaksManager.cpp.

                                               {
     // check the parameter
     if( spec == NULL ) {
         return NULL;
     }
 
     // get peaks
     if( m_specPeaksMap.find( spec ) == m_specPeaksMap.end() ) {
         return NULL;
     }
     return &( m_specPeaksMap[ spec ] );
 }

Peaks * kome::objects::PeaksManager::getPeaks ( Chromatogram * chrom )

gets peaks of specified chromatogram

Parameters

[in] chrom chromatogram

Returns: peaks object (If NULL, peaks object is not created yet.)

Definition at line 57 of file PeaksManager.cpp.

                                                    {
     // check the parameter
     if( chrom == NULL ) {
         return NULL;
     }
 
     // get peaks
     if( m_chromPeaksMap.find( chrom ) == m_chromPeaksMap.end() ) {
         return NULL;
     }
     return &( m_chromPeaksMap[ chrom ] );
 }

Peaks2D * kome::objects::PeaksManager::getPeaks ( DataGroupNode * group )

gets peak of specified spectrum group

Parameters

[in] group spectrum group

Returns: peaks object (If NULL, peaks object is not created yet.)

Definition at line 71 of file PeaksManager.cpp.

                                                       {
     // check the parameter
     if( group == NULL ) {
         return NULL;
     }
 
     // get peaks
     if( m_2dPeaksMap.find( group ) == m_2dPeaksMap.end() ) {
         return NULL;
     }
     return &( m_2dPeaksMap[ group ] );
 }

bool kome::objects::PeaksManager::hasPeaks ( Spectrum * spec )

judges whether peaks object of specified spectrum exists

Parameters

[in] spec spectrum

Returns: If true, peaks object of specified spectrum exists.

Definition at line 146 of file PeaksManager.cpp.

                                             {
     return ( m_specPeaksMap.find( spec ) != m_specPeaksMap.end() );
 }

bool kome::objects::PeaksManager::hasPeaks ( Chromatogram * chrom )

judges whether peaks object of specified chromatogram exists

Parameters

[in] chrom chromatogram

Returns: If true, peaks object of specified chromatogtram exists.

Definition at line 151 of file PeaksManager.cpp.

                                                  {
     return ( m_chromPeaksMap.find( chrom ) != m_chromPeaksMap.end() );
 }

bool kome::objects::PeaksManager::hasPeaks ( DataGroupNode * group )

judges whether peaks object of specified spectrum group exists

Parameters

[in] group spectrum group

Returns: If true, peaks object of specified spectrum group exists.

Definition at line 156 of file PeaksManager.cpp.

                                                   {
     return ( m_2dPeaksMap.find( group ) != m_2dPeaksMap.end() );
 }

void kome::objects::PeaksManager::onCloseSample	(	Sample *	sample,
		const bool	deleting
	)

protectedvirtual

This method is called when a sample is closed. (override method)

Parameters

[in]	sample	sample object to be closed
[in]	deleting	If true, the specified object is being deleted now.

Reimplemented from kome::objects::DefaultDataManager.

Definition at line 182 of file PeaksManager.cpp.

                                                                       {
     // get spectra
     std::vector< Spectrum* > spectra;
     for( std::map< Spectrum*, Peaks >::iterator it = m_specPeaksMap.begin();
             it != m_specPeaksMap.end(); it++ ) {
         // spectrum
         Spectrum* spec = (*it).first;
         if( spec->getSample() == sample ) {
             spectra.push_back( spec );
         }
     }
 
     // erase spectrum peaks
     for( unsigned int i = 0; i < spectra.size(); i++ ) {
         Spectrum* spec = spectra[ i ];
         m_specPeaksMap[ spec ].clearPoints();
         m_specPeaksMap.erase( spec );
     }
 
     // get chromatograms
     std::vector< Chromatogram* > chroms;
     for( std::map< Chromatogram*, Peaks >::iterator it = m_chromPeaksMap.begin();
             it != m_chromPeaksMap.end(); it++ ) {
         // chromatogram
         Chromatogram* chrom = (*it).first;
         if( chrom->getSample() == sample ) {
             chroms.push_back( chrom );
         }
     }
 
     // erase chromatogram peaks
     for( unsigned int i = 0; i < chroms.size(); i++ ) {
         Chromatogram* chrom = chroms[ i ];
         m_chromPeaksMap[ chrom ].clearPoints();
         m_chromPeaksMap.erase( chrom );
     }
 
     // get spectrum groups
     std::vector< DataGroupNode* > groups;
     for( std::map< DataGroupNode*, Peaks2D >::iterator it = m_2dPeaksMap.begin();
             it != m_2dPeaksMap.end(); it++ ) {
         // spectrum group
         DataGroupNode* group = (*it).first;
         if( group->getSample() == sample ) {
             groups.push_back( group );
         }
     }
 
     // erase 2d peaks
     for( unsigned int i = 0; i < groups.size(); i++ ) {
         DataGroupNode* group = groups[ i ];
 
         Peaks2D& peaks = m_2dPeaksMap[ group ];
         peaks.clearClusters();
         peaks.clearPeaks();
 
         m_2dPeaksMap.erase( group );
     }
 }

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void kome::objects::PeaksManager::updatePeaks	(	Spectrum &	spec,
		Peaks *	peaks,
		std::vector< PeakElement > &	addPeaks
	)

update peaks

Parameters

[in]	spec	spectrum object
[in]	peaks	peaks object
[in]	addPeaks	peak element object to add

Definition at line 243 of file PeaksManager.cpp.

                                                                                               {
     if( peaks == NULL ) {
         peaks = createPeaks( &spec );
     }
     else {
         peaks->clearPoints();
     }
 
     for( unsigned int i=0; i < addPeaks.size(); i++ ){
         PeakElement* peakElement = peaks->createPeak( addPeaks[i].getX(), addPeaks[i].getY() );
         if( peakElement != NULL ){
             peakElement->setLeft( addPeaks[i].getLeftX(), addPeaks[i].getLeftY() );
             peakElement->setRight( addPeaks[i].getRightX(), addPeaks[i].getRightY() );
             peakElement->setApex( addPeaks[i].getApexX(), addPeaks[i].getApexY() );
             peakElement->setId( addPeaks[i].getId() );
         }
     }
 }

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Member Data Documentation

std::map< DataGroupNode*, Peaks2D > kome::objects::PeaksManager::m_2dPeaksMap

protected

2D peaks

Definition at line 63 of file PeaksManager.h.

std::map< Chromatogram*, Peaks > kome::objects::PeaksManager::m_chromPeaksMap

protected

chromatogram peaks

Definition at line 60 of file PeaksManager.h.

std::map< Spectrum*, Peaks > kome::objects::PeaksManager::m_specPeaksMap

protected

spectrum peaks

Definition at line 57 of file PeaksManager.h.

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

DataObjects/PeaksManager.h
DataObjects/PeaksManager.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

Member Data Documentation