spectrum information management class More...

#include <Spectrum.h>

Inheritance diagram for kome::objects::Spectrum:

Collaboration diagram for kome::objects::Spectrum:

Classes
struct	PrecursorInfo
	precursor information More...

Public Types
enum	Polarity { POLARITY_UNKNOWN = 0, POLARITY_POSITIVE = 1, POLARITY_NEGATIVE = 2 }
	polarity definition

Public Member Functions
	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...

Static Public Member Functions
static bool	isCommonProperty (const char *key)
	check whther the specified property key is common property or not More...

Protected Member Functions
virtual void	onGetXYData (kome::core::XYData *const xyData, const double minX, const double maxX)=0
	This method is called by getXYData method. (abstract method) More...

virtual void	onGetXRange (double minX, double maxX)=0
	This method is called by getMinX or getMaxX method. (abstract method) More...

virtual double	onGetTotalIntensity (const double minX, const double maxX)=0
	This method is called by getTotalIntensity method. (abstract method) More...

virtual double	onGetMaxIntensity (const double minX, const double maxX)=0
	This method is called by getMaxIntensity method. (abstract 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...

bool	firstAccessProcess (void)
	method for processing when accessing the first item of this class More...

Protected Attributes
Spectrum *	m_orgSpec

bool	m_op

int	m_specId

Static Protected Attributes
static std::vector< std::string >	m_commonProps

Detailed Description

spectrum information management class

Definition at line 30 of file Spectrum.h.

Constructor & Destructor Documentation

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

constructor

Parameters

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

Definition at line 42 of file Spectrum.cpp.

                                                      {
     // initialize
     m_sample = sample;
     m_name = NVL( name, "" );
 
     m_rt.start = -1.0;
     m_rt.end = -1.0;
 
     m_bpm = -1.0;
 
     m_msStage = 1;
     m_parentSpec = NULL;
     m_chrom = false;
 
     m_charge = 0;
 
     m_group = NULL;
     m_scanNumber = -1;
 
     m_polarity = POLARITY_UNKNOWN;
     m_centroidMode = false;
 
     m_resolution = -1.0;
 
     m_orgSpec = NULL;
     m_op = false;
 
     // reserve properties
     isCommonProperty( NULL );
 
     for( unsigned int i = 0; i < m_commonProps.size(); i++ ) {
         m_props.setValue( m_commonProps[ i ].c_str(), "" );
     }
     m_props.setValue( "Name", m_name.c_str() );
 
     // issue spectrum id
     if( sample != NULL ){
         m_specId = sample->issueSpecId();
     }
 
     // visible flag
     m_visible = true;
     m_autoZeroPoints = true;
 
     // >>>>>> @Date:2013/07/16  <Add>   A.Ozaki
     m_strSpotId = FMT( "" );
     // <<<<<< @Date:2013/07/16  <Add>   A.Ozaki
 
 }

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Member Function Documentation

bool kome::objects::Spectrum::firstAccessProcess ( void )

protected

method for processing when accessing the first item of this class

Returns: If true, file reading success.

Definition at line 1252 of file Spectrum.cpp.

 {
     bool    bRet = true;
     if  ( isFirstAccess( ) && isRequestLoadData( ) )
     {
         bRet = loadData( );
         resetFirstAccess( );
     }
 
     return  bRet;
 }

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double kome::objects::Spectrum::getBasePeakMass ( )

gets base peak mass

Returns: base peak mass

Definition at line 581 of file Spectrum.cpp.

                                  {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     return m_bpm;
 }

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void kome::objects::Spectrum::getChildSpectra ( std::vector< Spectrum * > & children )

gets child spectra

Parameters

[out] children the array to store child spectra

Definition at line 855 of file Spectrum.cpp.

                                                                  {
     // sample
     Sample* smpl = getSample();
     if( smpl == NULL ) {
         return;
     }
 
     // get children
     if( m_children.size() == 0 ) {
         // spectra
         for( unsigned int i = 0; i < smpl->getNumberOfGroups(); i++ ) {
             DataGroupNode* group = smpl->getGroup( i );
             for( unsigned int j = 0; j < group->getNumberOfSpectra(); j++ ) {
                 Spectrum* spec = group->getSpectrum( j );
                 if( spec->getParentSpectrum() == this ) {
                     m_children.push_back( spec );
                 }
             }
         }
     }
 
     // store
     for( unsigned int i = 0; i < m_children.size(); i++ ) {
         children.push_back( m_children[ i ] );
     }
 }

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const char * kome::objects::Spectrum::getCollisionEnergy ( )

gets the collision energy

Returns: collision energy

Definition at line 963 of file Spectrum.cpp.

                                          {
     return m_collisionEnergy.c_str();
 }

double kome::objects::Spectrum::getEndRt ( )

gets the end of retention time

Returns: the end of retention time

Definition at line 197 of file Spectrum.cpp.

                           {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     return m_rt.end;
 }

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DataGroupNode * kome::objects::Spectrum::getGroup ( )

gets spectrum group

Returns: spectrum group

Definition at line 898 of file Spectrum.cpp.

                                   {
     return m_group;
 }

const char * kome::objects::Spectrum::getIcon ( )

gets icon name

Returns: icon name

Definition at line 273 of file Spectrum.cpp.

                               {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     return m_icon.c_str();
 }

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int kome::objects::Spectrum::getId ( )

gets spectrum id

Returns: spectrum id

Definition at line 1136 of file Spectrum.cpp.

                    {
     return m_specId;
 }

double kome::objects::Spectrum::getMaxIntensity	(	const double	minX = `-1.0`,
		const double	maxX = `-1.0`
	)

gets max intensity in specified range

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

Definition at line 548 of file Spectrum.cpp.

                                                                        {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     // check member
     if( minX < 0.0 && maxX < 0.0 ) {
         if( m_bpi ) {
             return m_bpi.get();
         }
     }
 
     // get max intensity
     double intensity = onGetMaxIntensity( minX, maxX );
 
     // set bpc
     if( minX < 0.0 && maxX < 0.0 ) {
         setMaxIntensity( intensity );
     }
 
     return intensity;
 }

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double kome::objects::Spectrum::getMaxX ( )

gets max x

Returns: max x

Definition at line 489 of file Spectrum.cpp.

                          {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     // check the member
     if( !m_maxX ) {
         double minX = double();
         double maxX = double();
 
         onGetXRange( &minX, &maxX );
 
         setXRange( minX, maxX );
     }
 
     return m_maxX.get();
 }

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double kome::objects::Spectrum::getMinX ( )

gets min x

Returns: min x

Definition at line 461 of file Spectrum.cpp.

                          {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     // check the member
     if( !m_minX ) {
         double minX = double();
         double maxX = double();
 
         onGetXRange( &minX, &maxX );
 
         setXRange( minX, maxX );
     }
 
     return m_minX.get();
 }

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int kome::objects::Spectrum::getMsStage ( )

gets ms stage

Returns: ms stage

Definition at line 634 of file Spectrum.cpp.

                          {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     return m_msStage;
 }

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

gets spectrum name

Returns: spectrum name

Definition at line 123 of file Spectrum.cpp.

                               {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     return m_name.c_str();
 }

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bool kome::objects::Spectrum::getOperationFlag ( )

inline

gets the operation flag value

Returns: operation flag value

Definition at line 202 of file Spectrum.h.

202 { return m_op; }

kome::objects::Spectrum::m_op

bool m_op

Definition: Spectrum.h:165

Spectrum * kome::objects::Spectrum::getOrgSpectrum ( )

gets original spectrum

Returns: original spectrum

Definition at line 1003 of file Spectrum.cpp.

                                    {
     if( m_orgSpec == NULL ) {
         m_orgSpec = this;
     }
 
     return m_orgSpec;
 }

Spectrum * kome::objects::Spectrum::getParentSpectrum ( )

gets parent spectrum

Returns: parent spectrum. (If this spectrum has no parent, this method returns NULL.)

Definition at line 850 of file Spectrum.cpp.

                                       {
     return m_parentSpec;
 }

Polarity kome::objects::Spectrum::getPolarity ( )

gets polarity

Returns: polarity

Definition at line 930 of file Spectrum.cpp.

                                        {
     return m_polarity;
 }

double kome::objects::Spectrum::getPrecursor ( const int stage )

gets precursor

Parameters

[in] stage MS stage of precursor ion spectrum

Returns: precursor

Definition at line 683 of file Spectrum.cpp.

                                                {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     for( unsigned int i = 0; i < m_precursor.size(); i++ ) {
         if( m_precursor[ i ].stage == stage ) {
             return m_precursor[ i ].precursor;
         }
     }
 
     return -1.0;
 }

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double kome::objects::Spectrum::getPrecursor ( )

gets the precursor mass of precursor ion spectrum.

Returns: precursor mass

Definition at line 695 of file Spectrum.cpp.

                               {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     int stage = ( m_msStage > 1 ? ( m_msStage - 1 ) : -1 );
     return getPrecursor( stage );
 }

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int kome::objects::Spectrum::getPrecursorCharge ( )

gets the precursor charge

Returns: precursor charge

Definition at line 816 of file Spectrum.cpp.

                                  {
     return m_charge;
 }

double kome::objects::Spectrum::getPrecursorIntensity ( const int stage )

gets the precursor intensity

Parameters

[in] stage MS stage of precursor ion spectrum

Returns: precursor intensity

Definition at line 749 of file Spectrum.cpp.

                                                         {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     // get intensity
     double intensity = -1.0;
     for( unsigned int i = 0; i < m_precursor.size(); i++ ) {
         if( m_precursor[ i ].stage == stage ) {
             intensity = m_precursor[ i ].intensity;
         }
     }
     if( intensity >= 0.0 ) {
         return intensity;
     }
 
     // get from parent spectrum
     Spectrum* parent = getParentSpectrum();
     double precursor = getPrecursor( stage );
     if( precursor < 0.0 ) {
         return -1.0;
     }
 
     std::set< Spectrum* > parentSet;
     parentSet.insert( this );
     parentSet.insert( parent );
     while( parent != NULL && parent->getMsStage() != stage ) {
         parent = parent->getParentSpectrum();
         if( parentSet.find( parent ) == parentSet.end() ) {
             parentSet.insert( parent );
         }
         else {
             parent = NULL;
         }
     }
 
     if( parent != NULL ) {
         intensity = 0.0;
         kome::core::DataPoints dps;
         parent->getXYData( &dps, precursor - 0.5, precursor + 0.5, false );
 
         for( unsigned int i = 0; i < dps.getLength(); i++ ) {
             intensity = std::max( intensity, dps.getY( i ) );
         }   
         setPrecursorIntensity( stage, intensity );
     }
 
     return intensity;
 }

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double kome::objects::Spectrum::getPrecursorIntensity ( )

gets the precursor intensity of the precursor ion spectrum.

Returns: the precursor intensity

Definition at line 797 of file Spectrum.cpp.

                                        {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     int stage = ( m_msStage > 1 ? ( m_msStage - 1 ) : -1 );
     return getPrecursorIntensity( stage );
 }

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

gets properties

Returns: properties

Definition at line 968 of file Spectrum.cpp.

                                             {
     return m_props;
 }

void kome::objects::Spectrum::getProperties ( kome::core::Properties & properties )

gets spectrum and spectrum group properties

Parameters

[out] properties properties object to store properties

Definition at line 1012 of file Spectrum.cpp.

                                                              {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     // get spectrum properties
     for( unsigned int i = 0; i < m_props.getNumberOfProperties(); i++ ) {
         properties.setValue( m_props.getKey( i ), m_props.getValue( i ) );
     }
 
     // get peak information
     PeaksManager& pkMgr = PeaksManager::getInstance();
     Peaks* peaks = pkMgr.getPeaks( this );
     if( peaks != NULL ) {
         int peakNum = peaks->getLength();
         double precursor = peaks->getPrecursor();
         std::string chargeStr;
         for( unsigned int i = 0; i < peaks->getNumberOfCharges(); i++ ) {
             int charge = peaks->getCharge( i );
             if( charge > 0 ) {
                 if( !chargeStr.empty() ) {
                     chargeStr.append( ", " );
                 }
             }
             chargeStr.append( FMT( "%d", charge ) );
         }
 
         properties.setIntValue( "Peaks Count", peakNum );
         if( precursor < 0.0 ) {
             properties.setValue( "Calculated Precursor", "" );
         }
         else {
             properties.setDoubleValue( "Calculated Precursor", precursor );
         }
         properties.setValue( "Calculated Precursor Charge", chargeStr.c_str() );
     }
 
     // get group properties
     DataGroupNode* group = m_group;
 
     while( group != NULL ) {
         for( unsigned int i = 0; i < group->getProperties().getNumberOfProperties(); i++ ) {
             properties.setValue(
                 group->getProperties().getKey( i ),
                 group->getProperties().getValue( i )
             );
         }
         group = group->getParentGroup();
     }
 }

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double kome::objects::Spectrum::getResolution ( )

gets resolution

Returns: resolution

Definition at line 952 of file Spectrum.cpp.

                                {
     return m_resolution;
 }

double kome::objects::Spectrum::getRt ( )

gets retention time

Returns: retention time

Definition at line 184 of file Spectrum.cpp.

                        {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     double rt = ( m_rt.start + m_rt.end ) / 2.0;
     return rt;
 }

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Sample * kome::objects::Spectrum::getSample ( )

gets the sample that has this spectrum

Returns: sample object

Definition at line 108 of file Spectrum.cpp.

                             {
     return m_sample;
 }

int kome::objects::Spectrum::getScanNumber ( )

gets scan number

Returns: scan number

Definition at line 915 of file Spectrum.cpp.

                             {
     return m_scanNumber;
 }

const char * kome::objects::Spectrum::getSpecType ( )

gets spectrum type

Returns: spectrum type

Definition at line 209 of file Spectrum.cpp.

                                   {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     return m_specType.c_str();
 }

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const char * kome::objects::Spectrum::getSpotId ( void )

get spot id

Returns: string of spot id

Definition at line 1153 of file Spectrum.cpp.

 {
     firstAccessProcess( );
     return  m_strSpotId.c_str( );
 }

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double kome::objects::Spectrum::getStartRt ( )

gets the start of retention time

Returns: the start of retention time

Definition at line 191 of file Spectrum.cpp.

                             {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     return m_rt.start;
 }

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const char * kome::objects::Spectrum::getTitle ( )

gets spectrum title

Returns: spectrum title

Definition at line 222 of file Spectrum.cpp.

                                {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
 
     if( m_title.empty() ) {
         std::string name = m_name;
         std::string values;
 
         int scanNum = getScanNumber();
         if( scanNum >= 0 ) {
             if( !values.empty() ) {
                 values.append( "," );
             }
             values.append( FMT( "scanNum=%d", scanNum ) );
         }
 
         double rt = getRt();
         if( rt >= 0.0 ) {
             if( !values.empty() ) {
                 values.append( "," );
             }
             values.append( FMT( "rt=%.2f", rt ) );
         }
 
         double prec = getPrecursor();
         if( prec >= 0.0 ) {
             if( !values.empty() ) {
                 values.append( "," );
             }
             values.append( FMT( "precursor=%.2f", prec ) );
         }
 
         if( values.empty() ) {
             m_title = name;
         }
         else if( name.empty() ) {
             m_title = values;
         }
         else {
             m_title = FMT( "%s: %s", name.c_str(), values.c_str() );
         }
     }
 
     return m_title.c_str();
 }

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double kome::objects::Spectrum::getTotalIntensity	(	const double	minX = `-1.0`,
		const double	maxX = `-1.0`
	)

gets total intensity in specified range

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

Definition at line 516 of file Spectrum.cpp.

                                                                          {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     // check member
     if( minX < 0.0 && maxX < 0.0 ) {
         if( m_tic ) {
             return m_tic.get();
         }
     }
 
     // get total intensity
     double intensity = onGetTotalIntensity( minX, maxX );
 
     // set tic
     if( minX < 0.0 && maxX < 0.0 ) {
         setTotalIntensity( intensity );
     }
 
     return intensity;
 }

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

gets user properties

Returns: user properties

Definition at line 993 of file Spectrum.cpp.

                                                 {
     return m_userProps;
 }

void kome::objects::Spectrum::getUserProperties ( kome::core::Properties & userProperties )

gets spectrum and spectrum group user properties

Parameters

[out] userProperties userProperties object to store user properties

Definition at line 1061 of file Spectrum.cpp.

                                                                      {
     firstAccessProcess( );          // @Date:2013/07/16 <Add>   A.Ozaki
     // get spectrum user properties
     for( unsigned int i = 0; i < m_userProps.getNumberOfProperties(); i++ ) {
         userProperties.setValue( m_userProps.getKey( i ), m_userProps.getValue( i ) );
     }
 
     // get group user properties
     DataGroupNode* group = m_group;
 
     while( group != NULL ) {
         for( unsigned int i = 0; i < group->getUserProperties().getNumberOfProperties(); i++ ) {
             userProperties.setValue(
                 group->getUserProperties().getKey( i ),
                 group->getUserProperties().getValue( i )
             );
         }
         group = group->getParentGroup();
     }
 }

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kome::core::XYData * kome::objects::Spectrum::getXYData ( )

gets xy data from data manager

Returns: xy data object

Definition at line 279 of file Spectrum.cpp.

                                     {
     PointsManager& ptMgr = PointsManager::getInstance();
 
     return ptMgr.getXYData( this );
 }

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void kome::objects::Spectrum::getXYData	(	kome::core::XYData *const	xyData,
		const bool	op
	)

gets data points

Parameters

[out]	xyData	the object to store data points
[in]	op	If true, getting operated data points

Definition at line 293 of file Spectrum.cpp.

                                                                       {
     // get data points
     getXYData( xyData, -1.0, -1.0, op );
 
     // operation
     if( op ) {
         // get operations
         PointsManager& ptMgr = PointsManager::getInstance();
         for( unsigned int i = 0; i < ptMgr.getNumberOfOperations( this ); i++ ) {
             XYDataOperation* operation = ptMgr.getOperation( this, i );
 
             operation->update( *xyData, *xyData, *this );
         }
     }
 }

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void kome::objects::Spectrum::getXYData	(	kome::core::XYData *const	xyData,
		const double	minX,
		const double	maxX,
		const bool	zero
	)

gets data points that spectrum has

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.)
[in]	zero	zero intensities insertion flag

Definition at line 310 of file Spectrum.cpp.

                                                                                                               {
     // check parameter
     if( xyData == NULL ) {
         return;
     }
 
     // gets data points
     kome::core::DataPoints dps;
     onGetXYData( &dps, minX, maxX );
 
     // correct data points
     if( minX < 0.0 && maxX < 0.0 ) {
         // get length
         unsigned int length = dps.getLength();
 
         // set x range
         double minXX = getMinX();
         double maxXX = getMaxX();
 
         // set total and max y
         if( !m_tic || !m_bpi || m_bpm < 0.0 ) {
             double tic = 0.0;
             double bpi = 0.0;
             double bpm = 0.0;
 
             for( unsigned int i = 0; i < length; i++ ) {
                 double x = dps.getX( i );
                 double y = dps.getY( i );
 
                 tic += y;
                 if( y > bpi ) {
                     bpi = y;
                     bpm = x;
                 }
             }
 
             if( !m_tic ) {
                 setTotalIntensity( tic );
             }
             if( !m_bpi ) {
                 setMaxIntensity( bpi );
             }
 
             if( m_bpm < 0.0 ) {
                 setBasePeakMass( bpm );
             }
         }
     }
     
     // get precursor intensity
     getPrecursorIntensity();
 
     // check the points
     if( dps.getLength() == 0 ) {
         return;
     }
 
     // zero points
     if( zero && m_autoZeroPoints ) {
         double minX = -1.0;
         if( m_minX ) {
             minX = m_minX.get();
         }
 
         double maxX = -1.0;
         if( m_maxX ) {
             maxX = m_maxX.get();
         }
 
         const double space = DEFAULT_RESOLUTION;
 
         // the first point
         double prevX = dps.getX( 0 );
         if( prevX > 0.0 && prevX > minX ) {
             prevX = prevX - space / 3.0;
             if( prevX < 0.0 ) {
                 prevX = 0.0;
             }
             if( prevX < minX ) {
                 prevX = minX;
             }
 
             xyData->addPoint( prevX, 0.0 );
         }
 
         // each points
         for( unsigned int i = 0; i < dps.getLength(); i++ ) {
             const double x = dps.getX( i );
             const double y = dps.getY( i );
 
             const double d = x - prevX;
 
             if( d > space ) {
                 const double startX = prevX + space / 3.0;
                 const double endX = x - space / 3.0;
 
                 xyData->addPoint( startX, 0.0 );
 
                 const int num = (int)( ( endX - startX ) / space );
 
                 for( int j = 0; j < num; j++ ) {
                     double midX = startX + (double)j * ( endX - startX ) / (double)( num + 2 );
                     if( midX > startX && midX < endX ) {
                         xyData->addPoint( midX, 0.0 );
                     }
                 }
 
                 xyData->addPoint( endX, 0.0 );
             }
 
             xyData->addPoint( x, y );
 
             prevX = x;
         }
 
         // last point
         if( maxX < 0.0 || prevX < maxX ) {
             prevX = prevX + space / 3.0;
             if( maxX >= 0.0 && prevX > maxX ) {
                 prevX = maxX;
             }
 
             xyData->addPoint( prevX, 0.0 );
         }
     }
     else {
         for( unsigned int i = 0; i < dps.getLength(); i++ ) {
             xyData->addPoint( dps.getX( i ), dps.getY( i ) );
         }
     }
 }

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bool kome::objects::Spectrum::hasChromatogram ( )

judges whether this spectrum has chromatogram

Returns: where this spectrum has chromatogram

Definition at line 888 of file Spectrum.cpp.

                                {
     return m_chrom;
 }

bool kome::objects::Spectrum::isAutoZeroPoints ( )

gets auto zero points flag value

Returns: auto zero points flag value

Definition at line 988 of file Spectrum.cpp.

                                 {
     return m_autoZeroPoints;
 }

bool kome::objects::Spectrum::isCentroidMode ( )

judget wheter this spectrum is centroid mode

Returns: If true, this spectrum is centroid mode.

Definition at line 941 of file Spectrum.cpp.

                               {
     return m_centroidMode;
 }

static bool kome::objects::Spectrum::isCommonProperty ( const char * key )

static

check whther the specified property key is common property or not

Parameters

[in] key parameter key

Returns: If true, specified key is common property key

Definition at line 1083 of file Spectrum.cpp.

                                                  {
     // common properties
     const char* keys[] = {
         "Name",
         "RT",
         "Start RT",
         "End RT",
         "Low Mass",
         "High Mass",
         "TIC",
         "BPI",
         "BPM",
         "Stage",
         "Precursor",
         "Precursor Intensity",
         "Scan Number",
         "Polarity",
         "Centroid Mode",
         "Resolution",
         "Collision Energy",
         "Spectrum Type",
         "Title"
     };
 
     // create array
     if( m_commonProps.size() == 0 ) {
         const unsigned int num = sizeof( keys ) / sizeof( const char* );
 
         for( unsigned int i = 0; i < num; i++ ) {
             m_commonProps.push_back( keys[ i ] );
         }
     }
 
     // check the key
     if( key == NULL ) {
         return false;
     }
 
     for( unsigned int i = 0; i < m_commonProps.size(); i++ ) {
         if( m_commonProps[ i ].compare( key ) == 0 ) {
             return true;
         }
     }
 
     return false;
 }

bool kome::objects::Spectrum::isFirstAccess ( void )

check the flag of first access

Returns: If true, enable flag of first access

Definition at line 1198 of file Spectrum.cpp.

 {
     return  onIsFirstAccess( );
 }

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bool kome::objects::Spectrum::isRequestLoadData ( void )

check the flag of request load data

Returns: If true, enable flag of request load data

Definition at line 1176 of file Spectrum.cpp.

 {
     return  onIsRequestLoadData( );
 }

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bool kome::objects::Spectrum::isVisible ( )

gets the visible flag value

Returns: visible flag value

Definition at line 978 of file Spectrum.cpp.

                          {
     return m_visible;
 }

bool kome::objects::Spectrum::loadData ( void )

load data

Returns: If true, file reading success.

Definition at line 1204 of file Spectrum.cpp.

 {
     return  onLoadData( );
 }

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double kome::objects::Spectrum::onGetMaxIntensity	(	const double	minX,
		const double	maxX
	)

protectedpure virtual

This method is called by getMaxIntensity method. (abstract 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

Implemented in kome::operation::TransformedSpectrum, kome::objects::AveragedSpectrum, kome::objects::OverlappingSpectrum, and kome::operation::ManipulatedSpectrum.

double kome::objects::Spectrum::onGetTotalIntensity	(	const double	minX,
		const double	maxX
	)

protectedpure virtual

This method is called by getTotalIntensity method. (abstract 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

Implemented in kome::operation::TransformedSpectrum, kome::objects::AveragedSpectrum, kome::objects::OverlappingSpectrum, and kome::operation::ManipulatedSpectrum.

void kome::objects::Spectrum::onGetXRange	(	double *	minX,
		double *	maxX
	)

protectedpure virtual

This method is called by getMinX or getMaxX method. (abstract method)

Parameters

[out]	minX	the pointer to store minimum x value
[out]	maxX	the pointer to store maximum x value

Implemented in kome::operation::TransformedSpectrum, kome::objects::AveragedSpectrum, kome::objects::OverlappingSpectrum, and kome::operation::ManipulatedSpectrum.

void kome::objects::Spectrum::onGetXYData	(	kome::core::XYData *const	xyData,
		const double	minX,
		const double	maxX
	)

protectedpure virtual

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

Implemented in kome::operation::TransformedSpectrum, kome::objects::AveragedSpectrum, kome::objects::OverlappingSpectrum, and kome::operation::ManipulatedSpectrum.

bool kome::objects::Spectrum::onIsFirstAccess ( void )

protectedvirtual

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

Returns: If true, the first accessing.

Reimplemented in kome::operation::TransformedSpectrum, and kome::operation::ManipulatedSpectrum.

Definition at line 1240 of file Spectrum.cpp.

 {
     return  false;
 }

bool kome::objects::Spectrum::onIsRequestLoadData ( void )

protectedvirtual

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

Returns: If true, file read request is valid.

Reimplemented in kome::operation::TransformedSpectrum, and kome::operation::ManipulatedSpectrum.

Definition at line 1222 of file Spectrum.cpp.

 {
     return  false;
 }

bool kome::objects::Spectrum::onLoadData ( void )

protectedvirtual

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

Returns: If true, file reading success.

Reimplemented in kome::operation::TransformedSpectrum, and kome::operation::ManipulatedSpectrum.

Definition at line 1246 of file Spectrum.cpp.

 {
     return  true;
 }

void kome::objects::Spectrum::setAutoZeroPoints ( const bool autoZero )

sets auto zero points flag value

Parameters

[in] autoZero auto zero points flag value.

Definition at line 983 of file Spectrum.cpp.

                                                       {
     m_autoZeroPoints = autoZero;
 }

void kome::objects::Spectrum::setBasePeakMass ( const double mass )

sets base peak mass

Parameters

[in] mass base peak mass

Definition at line 569 of file Spectrum.cpp.

                                                   {
     if( mass >= 0.0 ) {
         m_props.setDoubleValue( "BPM", mass );
     }
     else {
         m_props.setValue( "BPM", "" );
     }
 
     m_bpm = mass;
 }

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void kome::objects::Spectrum::setCentroidMode ( const bool centroidMode )

sets centroid mode or not

Parameters

[in] centroidMode If true, this spectrum is centroid mode.

Definition at line 935 of file Spectrum.cpp.

                                                         {
     m_props.setBoolValue( "Centroid Mode", centroidMode );
     m_centroidMode = centroidMode;
 }

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void kome::objects::Spectrum::setCollisionEnergy ( const char * collisionEnergy )

sets the collision energy

Parameters

[in] collisionEnergy collision energy

Definition at line 957 of file Spectrum.cpp.

                                                                {
     m_props.setValue( "Collision Energy", NVL( collisionEnergy, "" ) );
     m_collisionEnergy = NVL( collisionEnergy, "" );
 }

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void kome::objects::Spectrum::setEndRt ( const double rt )

sets end retention time

Parameters

[in] rt end retention time

Definition at line 172 of file Spectrum.cpp.

                                          {
     if( rt >= 0.0 ) {
         m_props.setDoubleValue( "End RT", rt );
     }
     else {
         m_props.setValue( "End RT", "" );
     }
 
     m_rt.end = rt;
 }

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void kome::objects::Spectrum::setGroup ( DataGroupNode * group )

sets spectrum group

Parameters

[in] group spectrum group

Definition at line 893 of file Spectrum.cpp.

                                               {
     m_group = group;
 }

void kome::objects::Spectrum::setHasChromatogram ( const bool chromatogram )

sets wheher this spectrum has chromatogram

Parameters

[in] chromatogram whether this spectrum has chromatogram

Definition at line 883 of file Spectrum.cpp.

                                                            {
     m_chrom = chromatogram;
 }

void kome::objects::Spectrum::setIcon ( const char * icon )

sets icon name

Returns: icon name

Definition at line 268 of file Spectrum.cpp.

                                          {
     m_icon = std::string( NVL( icon, "" ) );
 }

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

sets spectrum id

Parameters

[in] id spectrum id

Definition at line 1131 of file Spectrum.cpp.

                             {
     m_specId = id;
 }

void kome::objects::Spectrum::setMaxIntensity ( const double intensity )

sets max intensity of spectrum

Parameters

[in] intensity max intensity

Definition at line 537 of file Spectrum.cpp.

                                                        {
     if( intensity > 0.0 ) {
         m_props.setDoubleValue( "BPI", intensity );
         m_bpi = intensity;
     }
     else {
         m_props.setValue( "BPI", "" );
     }
 }

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void kome::objects::Spectrum::setMaxX ( const double maxX )

sets max x

Parameters

[in] maxX max x

Definition at line 477 of file Spectrum.cpp.

                                           {
     if( maxX >= 0.0 ) {
         m_props.setDoubleValue( "High Mass", maxX );
     }
     else {
         m_props.setValue( "High Mass", "" );
     }
 
     m_maxX = maxX;
 }

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void kome::objects::Spectrum::setMinX ( const double minX )

sets min x

Parameters

[in] minX min x

Definition at line 449 of file Spectrum.cpp.

                                           {
     if( minX >= 0.0 ) {
         m_props.setDoubleValue( "Low Mass", minX );
     }
     else  {
         m_props.setValue( "Low Mass", "" );
     }
 
     m_minX = minX;
 }

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void kome::objects::Spectrum::setMsStage ( const int stage )

sets ms stage

Parameters

[in] stage ms stage

Definition at line 587 of file Spectrum.cpp.

                                            {
     // properties
     if( stage > 0 ) {
         m_props.setIntValue( "Stage", stage );
     }
     else {
         m_props.setValue( "Stage", "" );
     }
 
     for( int i = 1; i < m_msStage; i++ ) {
         std::string key = FMT( "Precursor%d (Mass)", i );
         m_props.setValue( key.c_str(), "" );
 
         key = FMT( "Precursor%d (Intensity)", i );
         m_props.setValue( key.c_str(), "" );
     }
 
     // stage
     m_msStage = stage;
 
     // precursor
     int idx = -1;
     double prec = -1.0;
     double intensity = -1.0;
 
     for( unsigned int i = 0; i < m_precursor.size() && idx < 0; i++ ) {
         if( m_precursor[ i ].stage < 0 ) {
             idx = (int)i;
             prec = m_precursor[ i ].precursor;
             intensity = m_precursor[ i ].intensity;
         }
     }
 
     if( idx >= 0 ) {
         m_precursor.erase( m_precursor.begin() + idx );
 
         if( prec >= 0.0 ) {
             setPrecursor( stage - 1, prec );
         }
 
         if( intensity >= 0.0 ) {
             setPrecursorIntensity( stage - 1, intensity );
         }
     }
 }

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

sets spectrum name

Parameters

[in] name spectrum name

Definition at line 113 of file Spectrum.cpp.

                                          {
     m_name = std::string( NVL( name, "" ) ) ;
     if( m_title.empty() ) {
         setTitle( name );
     }
 
     m_props.setValue( "Name", m_name.c_str() );
 }

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void kome::objects::Spectrum::setOperationFlag ( const bool op )

inline

sets the operation flag value

Parameters

[in] op operation flag value

Definition at line 195 of file Spectrum.h.

195 { m_op = op; }

kome::objects::Spectrum::m_op

bool m_op

Definition: Spectrum.h:165

void kome::objects::Spectrum::setOrgSpectrum ( Spectrum * spec )

sets original spectrum

Parameters

[in] spec orignal spectrum

Definition at line 998 of file Spectrum.cpp.

                                               {
     m_orgSpec = spec;
 }

void kome::objects::Spectrum::setParentSpectrum ( Spectrum *const parent )

sets parent spectrum

Parameters

[in] parent parent spectrum oebject. (If this spectrum has no parent, this parameter is NULL.)

Definition at line 821 of file Spectrum.cpp.

                                                          {
     // set parent spectrum
     m_parentSpec = parent;
 
     // precursor
     std::set< Spectrum* > parentSet;
     parentSet.insert( this );
     parentSet.insert( parent );
     Spectrum* p = parent;
     while( p != NULL ) {
         int stage = p->getMsStage() - 1;
         if( stage > 0 ) {
             double precursor = getPrecursor( stage );
             if( precursor < 0.0 ) {
                 precursor = p->getPrecursor();
                 setPrecursor( stage, precursor );
             }
         }
         p = p->getParentSpectrum();
         if( parentSet.find( p ) == parentSet.end() ) {
             parentSet.insert( p );
         }
         else { 
             p = NULL;
         }
     }
 }

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void kome::objects::Spectrum::setPolarity ( Polarity polarity )

sets polarity

Parameters

[in] polarity polarity

Definition at line 920 of file Spectrum.cpp.

                                               {
     m_props.setValue(
         "Polarity",
         ( polarity == POLARITY_POSITIVE ? "+" : (polarity == POLARITY_NEGATIVE ? "-" : "" ) )
     );
 
     m_polarity = polarity;
 }

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void kome::objects::Spectrum::setPrecursor	(	const int	stage,
		const double	precursor
	)

sets precursor

Parameters

[in]	stage	MS stage of precursor ion spectrum.
[in]	precursor	precursor mass

Definition at line 640 of file Spectrum.cpp.

                                                                      {
     // property
     if( stage >= 1 ) {
         std::string key = FMT( "Precursor%d (Mass)", stage );
         m_props.setDoubleValue( key.c_str(), precursor );
 
         key = FMT( "Precursor%d (Intensity)", stage );
         if( !m_props.hasKey( key.c_str() ) ) {
             m_props.setValue( key.c_str(), "" );
         }
     }
 
     if( m_msStage > 1 && stage == m_msStage - 1 ) {
         m_props.setDoubleValue( "Precursor", precursor );
     }
 
     // search
     for( unsigned int i = 0; i < m_precursor.size(); i++ ) {
         if( m_precursor[ i ].stage == stage ) {
             m_precursor[ i ].precursor = precursor;
             return;
         }
     }
 
     // add
     m_precursor.resize( m_precursor.size() + 1 );
     m_precursor.back().stage = stage;
     m_precursor.back().intensity = -1.0;
     m_precursor.back().precursor = precursor;
 }

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void kome::objects::Spectrum::setPrecursor ( const double precursor )

sets precursor

Parameters

[in] precursor precursor mass

Definition at line 672 of file Spectrum.cpp.

                                                     {
     // stage
     if( m_msStage > 1 ) {
         setPrecursor( m_msStage - 1, precursor );
     }
     else {
         setPrecursor( -1, precursor );
     }
 }

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void kome::objects::Spectrum::setPrecursorCharge ( const int charge )

sets the precursor charge

Parameters

[in] charge precursor charge

Definition at line 804 of file Spectrum.cpp.

                                                     {
     m_charge = charge;
 
     if( charge > 0 ) {
         m_props.setIntValue( "Precursor Charge", charge );
     }
     else {
         m_props.setValue( "Precursor Charge", "" );
     }
 }

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void kome::objects::Spectrum::setPrecursorIntensity	(	const int	stage,
		const double	intensity
	)

sets precursor intensity

Parameters

[in]	stage	MS stage of precursor ion spectrum
[in]	intensity	precursor intensity

Definition at line 702 of file Spectrum.cpp.

                                                                               {
     // check parameters
     if( intensity < 0.0 ) {
         return;
     }
 
     // property
     if( stage >= 1 ) {
         std::string key = FMT( "Precursor%d (Mass)", stage );
         if( !m_props.hasKey( key.c_str() ) ) {
             m_props.setValue( key.c_str(), "" );
         }
 
         key = FMT( "Precursor%d (Intensity)", stage );
         m_props.setDoubleValue( key.c_str(), intensity );
     }
 
     if( m_msStage > 1 && stage == m_msStage - 1 ) {
         m_props.setDoubleValue( "Precursor Intensity", intensity );
     }
 
     // search
     for( unsigned int i = 0; i < m_precursor.size(); i++ ) {
         if( m_precursor[ i ].stage == stage ) {
             m_precursor[ i ].intensity = intensity;
             return;
         }
     }
 
     // add
     m_precursor.resize( m_precursor.size() + 1 );
     m_precursor.back().stage = stage;
     m_precursor.back().precursor = -1.0;
     m_precursor.back().intensity = intensity;
 }

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void kome::objects::Spectrum::setPrecursorIntensity ( const double intensity )

sets precursor intensity

Parameters

[in] intensity precursor intensity

Definition at line 739 of file Spectrum.cpp.

                                                              {
     if( m_msStage > 1 ) {
         setPrecursorIntensity( m_msStage - 1, intensity );
     }
     else {
         setPrecursorIntensity( -1, intensity );
     }
 }

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void kome::objects::Spectrum::setRequestLoadData ( void )

set the flag of request load data

reset the flag of request load data

Definition at line 1160 of file Spectrum.cpp.

 {
     onSetRequestLoadData( );
 
     return;
 }

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void kome::objects::Spectrum::setResolution ( const double resolution )

sets resolution

Parameters

[in] resolution resolution

Definition at line 946 of file Spectrum.cpp.

                                                       {
     m_props.setDoubleValue( "Resolution", resolution );
     m_resolution = resolution;
 }

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void kome::objects::Spectrum::setRt ( const double rt )

sets retention time

Parameters

[in] rt retention time

Definition at line 129 of file Spectrum.cpp.

                                       {
     // properties
     if( rt >= 0.0 ) {
         m_props.setDoubleValue( "RT", rt );
         m_props.setDoubleValue( "Start RT", rt );
         m_props.setDoubleValue( "End RT", rt );
     }
     else {
         m_props.setValue( "RT", "" );
         m_props.setValue( "Start RT", "" );
         m_props.setValue( "End RT", "" );
     }
 
     // RT
     setRt( rt, rt );
 }

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void kome::objects::Spectrum::setRt	(	const double	startRt,
		const double	endRt
	)

gets retention time

Parameters

[in]	startRt	the start retention time
[in]	endRt	the end retention time

Definition at line 147 of file Spectrum.cpp.

                                                                {
     if( startRt >= 0.0 && endRt >= 0.0 ) {
         m_props.setDoubleValue( "RT", ( startRt + endRt ) / 2.0 );
     }
     else {
         m_props.setValue( "RT", "" );
     }
 
     setStartRt( startRt );
     setEndRt( endRt );
 }

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void kome::objects::Spectrum::setScanNumber ( const int scan )

sets scan number

Parameters

[in] scan scan number

Definition at line 903 of file Spectrum.cpp.

                                              {
     if( scan >= 0 ) {
         m_props.setIntValue( "Scan Number", scan );
     }
     else {
         m_props.setValue( "Scan Number", "" );
     }
 
     m_scanNumber = scan;
 }

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void kome::objects::Spectrum::setSpecType ( const char * type )

sets spectrum type

Parameters

[in] type spectrum type

Definition at line 203 of file Spectrum.cpp.

                                              {
     m_specType = trimstring( type );
     m_props.setValue( "Spectrum Type", m_specType.c_str() );
 }

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void kome::objects::Spectrum::setStartRt ( const double rt )

sets start retention time

Parameters

[in] rt start retention time

Definition at line 160 of file Spectrum.cpp.

                                            {
     if( rt >= 0.0 ) {
         m_props.setDoubleValue( "Start RT", rt );
     }
     else {
         m_props.setValue( "Start RT", "" );
     }
 
     m_rt.start = rt;
 }

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void kome::objects::Spectrum::setTitle ( const char * title )

sets spectrum title

Parameters

[in] title spectrum title

Definition at line 215 of file Spectrum.cpp.

                                            {
     // title
     m_title = trimstring( title );
     m_props.setValue( "Title", m_title.c_str() );
 }

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void kome::objects::Spectrum::setTotalIntensity ( const double intensity )

sets total intensity of spectrum

Parameters

[in] intensity total intensity.

Definition at line 505 of file Spectrum.cpp.

                                                          {
     if( intensity > 0.0 ) {
         m_props.setDoubleValue( "TIC", intensity );
         m_tic = intensity;
     }
     else {
         m_props.setValue( "TIC", "" );
     }
 }

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void kome::objects::Spectrum::setVisible ( const bool visible )

sets the visible flag

Parameters

[in] visible visible flag value

Definition at line 973 of file Spectrum.cpp.

                                               {
     m_visible = visible;
 }

void kome::objects::Spectrum::setXRange	(	const double	minX,
		const double	maxX
	)

sets x range

Parameters

[in]	minX	min x
[in]	maxX	max x

Definition at line 443 of file Spectrum.cpp.

                                                                {
     setMinX( minX );
     setMaxX( maxX );
 }

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Member Data Documentation

std::vector< std::string > Spectrum::m_commonProps

staticprotected

common properties

Definition at line 169 of file Spectrum.h.

bool kome::objects::Spectrum::m_op

protected

operation flag

Definition at line 165 of file Spectrum.h.

Spectrum* kome::objects::Spectrum::m_orgSpec

protected

original spectrum

Definition at line 162 of file Spectrum.h.

int kome::objects::Spectrum::m_specId

protected

spectrum id

Definition at line 172 of file Spectrum.h.

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

DataObjects/Spectrum.h
DataObjects/Spectrum.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

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Detailed Description

Constructor & Destructor Documentation

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Member Data Documentation