group of spectrum management class More...

#include <DataGroupNode.h>

Inheritance diagram for kome::objects::DataGroupNode:

Collaboration diagram for kome::objects::DataGroupNode:

Public Member Functions
	DataGroupNode (Sample sample, const char name)
	constructor More...

virtual	~DataGroupNode ()
	destructor

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

int	getId ()
	gets gropu id More...

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

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

void	setGroupIndex (const int index)
	sets group index More...

int	getGroupIndex ()
	gets group index More...

DataGroupNode *	getParentGroup ()
	get parent spectrum group More...

DataGroupNode *	createChildGroup (const char *name)
	creates new child group object More...

void	removeChildGroup (DataGroupNode *child)
	removes child group More...

unsigned int	getNumberOfChildren ()
	gets the number of children More...

DataGroupNode *	getChild (const unsigned int index)
	gets child group More...

void	getDataSet (DataSet *dataSet)
	gets spectra that contains this group. (getSpectrum method cannot get spectra that belong to child group.) More...

void	setAutoScanNumber (const bool autoScanNumber)
	sets the auto scan number flag More...

bool	isAutoScanNumber ()
	gets the auto scan number flag More...

void	setSpecXTitle (const char *title)
	sets spectrum x axis title More...

const char *	getSpecXTitle ()
	gets spectrum x axis title More...

void	setSpecYTitle (const char *title)
	sets spectrum y axis title More...

const char *	getSpecYTitle ()
	gets spectrum y axis title More...

void	setChromXTitle (const char *title)
	sets chromatogram x axis title More...

const char *	getChromXTitle ()
	gets chromatogram x axis title More...

void	setChromYTitle (const char *title)
	sets chromatogram y axis title More...

const char *	getChromYTitle ()
	gets chromatogram y axis title More...

unsigned int	getLevel ()
	gets group level More...

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

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

virtual void	sortSpectra ()
	sorts spectra in retention time order (override method)

virtual void	insertSpectrum (Spectrum *spectrum, const int idx)
	adds spectrum to group (override method ) More...

virtual void	insertChromatogram (Chromatogram *chrom, const int idx)
	adds chromatogram (override method) More...

Public Member Functions inherited from kome::objects::DataSet
	DataSet ()
	constructor

	DataSet (DataGroupNode *group)
	constructor More...

virtual	~DataSet ()
	destructor

Sample *	getSample ()
	gets sample More...

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

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

Spectrum *	getSpectrum (const unsigned int index)
	gets the number of spectra More...

unsigned int	getNumberOfChromatograms ()
	gets the number of chromatograms More...

Chromatogram *	getChromatogram (const unsigned int index)
	gets chroamtogram More...

virtual void	clearSpectra ()
	clears spectra

virtual void	addSpectrum (Spectrum *spec)
	adds spectrum to group More...

virtual void	removeSpectrum (Spectrum *spec)
	removes spectrum More...

virtual void	clearChromatograms ()
	clears chromatograms

virtual void	addChromatogram (Chromatogram *chrom)
	adds chromatogram More...

virtual void	removeChromatogram (Chromatogram *chrom)
	removes chromatogram More...

Protected Member Functions
void	setParentDataGroupNode (DataGroupNode *parent)
	sets parent spectrum group More...

void	createDefaultChromatogram ()
	creates default chromatogram

Protected Attributes
DataGroupNode *	m_parent

std::string	m_name

int	m_index

short	m_level

std::vector< DataGroupNode * >	m_children

std::string	m_specXTitle

std::string	m_specYTitle

std::string	m_chromXTitle

std::string	m_chromYTitle

kome::core::Properties	m_properties

kome::core::Properties	m_userProperties

int	m_groupId

bool	m_autoScanNumber

Protected Attributes inherited from kome::objects::DataSet
Sample *	m_sample

DataGroupNode *	m_group

std::vector< Spectrum * >	m_spectra

std::vector< Chromatogram * >	m_chroms

Additional Inherited Members
Static Protected Member Functions inherited from kome::objects::DataSet
static bool	lessSpectrum (Spectrum spec0, Spectrum spec1)
	compare to sort spectra More...

Detailed Description

group of spectrum management class

Definition at line 33 of file DataGroupNode.h.

Constructor & Destructor Documentation

kome::objects::DataGroupNode::DataGroupNode	(	Sample *	sample,
		const char *	name
	)

constructor

Parameters

[in]	sample	sample object that has this spectrum group
[in]	name	spectrum group name

Definition at line 40 of file DataGroupNode.cpp.

                                                                : DataSet( NULL ) {
     // log
     LOG_TRACE( FMT( "Creating spectrum group... (%s)", NVL( name, "" ) ) );
 
     // initialize
     m_group = this;
     m_sample = sample;
     setName( name );
     m_index = -1;
     m_parent = NULL;
     m_autoScanNumber = true;
 
     // axis title
     m_specXTitle  = DEFAULT_SPEC_X_TITLE;
     m_specYTitle  = DEFAULT_SPEC_Y_TITLE;
     m_chromXTitle = DEFAULT_CHROM_X_TITLE;
     m_chromYTitle = DEFAULT_CHROM_Y_TITLE;
 
     // level
     m_level = 0;
     
     // issue group id
     if( sample != NULL ){
         m_groupId = sample->issueGroupId( sample );
     }
 }

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Member Function Documentation

DataGroupNode * kome::objects::DataGroupNode::createChildGroup ( const char * name )

creates new child group object

Parameters

[in] name child group name

Returns: the pointer to new child object

Definition at line 114 of file DataGroupNode.cpp.

                                                                 {
     // create child group object
     DataGroupNode* child = new DataGroupNode( m_sample, name );
     child->m_level = m_level + 1;
     child->setParentDataGroupNode( this );
 
     // add object to the array
     m_children.push_back( child );
 
     return child;
 }

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DataGroupNode * kome::objects::DataGroupNode::getChild ( const unsigned int index )

gets child group

Parameters

[in] index child group index

Returns: the pointer to the child group. (If index is illegal number, this method returns NULL.)

Definition at line 149 of file DataGroupNode.cpp.

                                                                  {
     // check the index
     if( index >= m_children.size() ) {
         return NULL;
     }
     return m_children[ index ];
 }

const char * kome::objects::DataGroupNode::getChromXTitle ( )

gets chromatogram x axis title

Returns: chromatogram x axis title

Definition at line 216 of file DataGroupNode.cpp.

                                           {
     return m_chromXTitle.c_str();
 }

const char * kome::objects::DataGroupNode::getChromYTitle ( )

gets chromatogram y axis title

Returns: chromatogram y axis title

Definition at line 226 of file DataGroupNode.cpp.

                                           {
     return m_chromYTitle.c_str();
 }

void kome::objects::DataGroupNode::getDataSet ( DataSet * dataSet )

gets spectra that contains this group. (getSpectrum method cannot get spectra that belong to child group.)

Parameters

[out] dataSet data set object to store spectrum information

Definition at line 158 of file DataGroupNode.cpp.

                                                  {
     // check parameter
     if( dataSet == NULL ) {
         return;
     }
 
     // get chromatograms
     for( unsigned int i = 0; i < m_chroms.size(); i++ ) {
         dataSet->addChromatogram( m_chroms[ i ] );
     }
 
     // get spectra
     for( unsigned int i = 0; i < m_spectra.size(); i++ ) {
         dataSet->addSpectrum( m_spectra[ i ] );
     }
 
     // gets spectra that belong to child group
     for( unsigned int i = 0; i < m_children.size(); i++ ) {
         m_children[ i ]->getDataSet( dataSet );
     }
 }

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int kome::objects::DataGroupNode::getGroupIndex ( )

gets group index

Returns: group index

Definition at line 104 of file DataGroupNode.cpp.

                                  {
     return m_index;
 }

int kome::objects::DataGroupNode::getId ( )

gets gropu id

Returns: group id

Definition at line 332 of file DataGroupNode.cpp.

                         {
     return m_groupId;
 }

unsigned int kome::objects::DataGroupNode::getLevel ( )

gets group level

Returns: group level

Definition at line 231 of file DataGroupNode.cpp.

                                      {
     return m_level;
 }

const char * kome::objects::DataGroupNode::getName ( )

gets group name

Returns: group name

Definition at line 94 of file DataGroupNode.cpp.

                                    {
     return m_name.c_str();
 }

unsigned int kome::objects::DataGroupNode::getNumberOfChildren ( )

gets the number of children

Returns: the number of children

Definition at line 144 of file DataGroupNode.cpp.

                                                 {
     return m_children.size();
 }

DataGroupNode * kome::objects::DataGroupNode::getParentGroup ( )

get parent spectrum group

Returns: parent spectrum group. (If this is root group, this method returns NULL.)

Definition at line 109 of file DataGroupNode.cpp.

                                              {
     return m_parent;
 }

kome::core::Properties & kome::objects::DataGroupNode::getProperties ( )

gets properties

Returns: properties

Definition at line 236 of file DataGroupNode.cpp.

                                                  {
     return m_properties;
 }

const char * kome::objects::DataGroupNode::getSpecXTitle ( )

gets spectrum x axis title

Returns: spectrum x axis title

Definition at line 196 of file DataGroupNode.cpp.

                                          {
     return m_specXTitle.c_str();
 }

const char * kome::objects::DataGroupNode::getSpecYTitle ( )

gets spectrum y axis title

Returns: spectrum y axis title

Definition at line 206 of file DataGroupNode.cpp.

                                          {
     return m_specYTitle.c_str();
 }

kome::core::Properties & kome::objects::DataGroupNode::getUserProperties ( )

gets user properties

Returns: properties

Definition at line 241 of file DataGroupNode.cpp.

                                                      {
     return m_userProperties;
 }

void kome::objects::DataGroupNode::insertChromatogram	(	Chromatogram *	chrom,
		const int	idx
	)

virtual

adds chromatogram (override method)

Parameters

[in]	chrom	chromatogram
[in]	idx	insert position

Reimplemented from kome::objects::DataSet.

Definition at line 306 of file DataGroupNode.cpp.

                                                                                       {
     // check the object
     if( chrom == NULL ) {
         return;
     }
 
     // insert
     m_chroms.insert( m_chroms.begin() + idx, chrom );
     chrom->setGroup( this );
 
     // delete
     for( int i = (int)m_chroms.size() - 1; i >= 0; i-- ) {
         Chromatogram* tmp = m_chroms[ i ];
         if( tmp->isAutoCreated() ) {
             m_chroms.erase( m_chroms.begin() + i );
             delete tmp;
         }
     }
 }

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void kome::objects::DataGroupNode::insertSpectrum	(	Spectrum *	spectrum,
		const int	idx
	)

virtual

adds spectrum to group (override method )

Parameters

[in]	spectrum	spectrum object to be added
[in]	idx	insert position

Reimplemented from kome::objects::DataSet.

Definition at line 284 of file DataGroupNode.cpp.

                                                                       {
     // check the parameter
     if( spectrum == NULL ) {
         return;
     }
 
     // set spectrum properties
     int scanNum = (int)m_spectra.size();
 
     if( spectrum->getScanNumber() < 0 && m_autoScanNumber ) {
         spectrum->setScanNumber( scanNum );
     }
     spectrum->setGroup( this );
 
     // insert spectrum
     m_spectra.insert( m_spectra.begin() + idx, spectrum );
 
     // default chromatogram
     createDefaultChromatogram();
 }

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bool kome::objects::DataGroupNode::isAutoScanNumber ( )

gets the auto scan number flag

Returns: auto scan number flag

Definition at line 186 of file DataGroupNode.cpp.

                                      {
     return m_autoScanNumber;
 }

void kome::objects::DataGroupNode::removeChildGroup ( DataGroupNode * child )

removes child group

Parameters

[in] child child group to be removed.

Definition at line 127 of file DataGroupNode.cpp.

                                                            {
     // index
     int idx = -1;
     for( int i = 0; i < (int)m_children.size() && idx < 0; i++ ) {
         DataGroupNode* tmp = m_children[ i ];
         if( tmp == child ) {
             idx = i;
         }
     }
 
     // removee
     if( idx >= 0 ) {
         m_children.erase( m_children.begin() + idx );
     }
 }

void kome::objects::DataGroupNode::setAutoScanNumber ( const bool autoScanNumber )

sets the auto scan number flag

Parameters

[in] autoScanNumber auto scan number flag

Definition at line 181 of file DataGroupNode.cpp.

                                                                  {
     m_autoScanNumber = autoScanNumber;
 }

void kome::objects::DataGroupNode::setChromXTitle ( const char * title )

sets chromatogram x axis title

Parameters

[in] title chromatogram x axis title

Definition at line 211 of file DataGroupNode.cpp.

                                                       {
     m_chromXTitle = std::string( NVL( title, "" ) );
 }

void kome::objects::DataGroupNode::setChromYTitle ( const char * title )

sets chromatogram y axis title

Parameters

[in] title chromatogram y axis title

Definition at line 221 of file DataGroupNode.cpp.

                                                       {
     m_chromYTitle = std::string( NVL( title, "" ) );
 }

void kome::objects::DataGroupNode::setGroupIndex ( const int index )

sets group index

Parameters

[in] index group index

Definition at line 99 of file DataGroupNode.cpp.

                                                    {
     m_index = index;
 }

void kome::objects::DataGroupNode::setId ( int id )

sets group id

Parameters

[in] id group id

Definition at line 327 of file DataGroupNode.cpp.

                                  {
     m_groupId = id;
 }

void kome::objects::DataGroupNode::setName ( const char * name )

sets group name

Parameters

[in] name group name

Definition at line 89 of file DataGroupNode.cpp.

                                               {
     m_name = std::string( NVL( name, "" ) );
 }

void kome::objects::DataGroupNode::setParentDataGroupNode ( DataGroupNode * parent )

protected

sets parent spectrum group

Parameters

[in] parent parent spectrum group

Definition at line 246 of file DataGroupNode.cpp.

                                                                   {
     m_parent = parent;
 }

void kome::objects::DataGroupNode::setSpecXTitle ( const char * title )

sets spectrum x axis title

Parameters

[in] title spectrum x axis title

Definition at line 191 of file DataGroupNode.cpp.

                                                      {
     m_specXTitle = std::string( NVL( title, "" ) );
 }

void kome::objects::DataGroupNode::setSpecYTitle ( const char * title )

sets spectrum y axis title

Parameters

[in] title spectrum y axis title

Definition at line 201 of file DataGroupNode.cpp.

                                                      {
     m_specYTitle = std::string( NVL( title, "" ) );
 }

Member Data Documentation

bool kome::objects::DataGroupNode::m_autoScanNumber

protected

auto scan number

Definition at line 85 of file DataGroupNode.h.

std::vector< DataGroupNode* > kome::objects::DataGroupNode::m_children

protected

the array of child groups

Definition at line 63 of file DataGroupNode.h.

std::string kome::objects::DataGroupNode::m_chromXTitle

protected

chromatogram x axis title

Definition at line 71 of file DataGroupNode.h.

std::string kome::objects::DataGroupNode::m_chromYTitle

protected

chromatogram y axis title

Definition at line 73 of file DataGroupNode.h.

int kome::objects::DataGroupNode::m_groupId

protected

group id

Definition at line 82 of file DataGroupNode.h.

int kome::objects::DataGroupNode::m_index

protected

group index

Definition at line 57 of file DataGroupNode.h.

short kome::objects::DataGroupNode::m_level

protected

level

Definition at line 60 of file DataGroupNode.h.

std::string kome::objects::DataGroupNode::m_name

protected

group name

Definition at line 54 of file DataGroupNode.h.

DataGroupNode* kome::objects::DataGroupNode::m_parent

protected

parent group

Definition at line 51 of file DataGroupNode.h.

kome::core::Properties kome::objects::DataGroupNode::m_properties

protected

properties

Definition at line 76 of file DataGroupNode.h.

std::string kome::objects::DataGroupNode::m_specXTitle

protected

spectrum x axis title

Definition at line 66 of file DataGroupNode.h.

std::string kome::objects::DataGroupNode::m_specYTitle

protected

spectrum y axis title

Definition at line 68 of file DataGroupNode.h.

kome::core::Properties kome::objects::DataGroupNode::m_userProperties

protected

user properties

Definition at line 79 of file DataGroupNode.h.

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

DataObjects/DataGroupNode.h
DataObjects/DataGroupNode.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation