kome::objects::Peaks Class Reference

peaks information class More...

#include <Peaks.h>

Inheritance diagram for kome::objects::Peaks:

Collaboration diagram for kome::objects::Peaks:

Public Member Functions
	Peaks ()
	constructor
	Peaks (const Peaks &peaks)
	copy constructor More...
virtual	~Peaks ()
	destructor
Peaks &	operator= (const Peaks &other)
	substitution operator More...
int	issueId (PeakElement *peakElement)
	to issue the peak id More...
PeakElement *	getPeakById (int id)
	gets peak element by peak id More...
void	clearCharge ()
	clears charge
void	addCharge (const short charge)
	adds charge More...
unsigned int	getNumberOfCharges ()
	gets the number of charges More...
short	getCharge (const unsigned int index)
	gets charge More...
void	setPrecursor (const double precursor)
	sets precursor More...
double	getPrecursor ()
	gets precursor More...
void	calcArea ()
	calculates area
void	setDataPoints (kome::core::XYData &xyData)
	sets data points More...
PeakElement *	createPeak (const double x, const double y)
	creates peak More...
PeakElement *	getPeak (const unsigned int index)
	gets peak More...
void	sort ()
	sorts peaks
Public Member Functions inherited from kome::core::XYData
	XYData ()
	constructor
virtual	~XYData ()
	destructor
double	getMinX ()
	gets minimum x More...
double	getMaxX ()
	gets maximum x More...
double	getMinY ()
	gets minimum y More...
double	getMaxY ()
	gets maximum y More...
void	clearPoints ()
	clear all data points
void	addPoint (const double x, const double y)
	adds point More...
void	insertPoint (const unsigned int index, const double x, const double y)
	insertts point More...
void	updatePoint (const unsigned int index, const double x, const double y)
	updates points More...
void	deletePoint (const unsigned int index)
	delete point More...
unsigned int	getLength ()
	gets the number of points @return the number of points
double	getX (const unsigned int index)
	gets x coordinate More...
double	getY (const unsigned int index)
	gets y coordinate More...
void	reserve (const unsigned int num)
	reserves enough contiguous memory of array More...
unsigned long	getVersion ()
	gets the version More...
int	searchIndex (const double x)
	searches index of specified x value. More...
int	getNearestIndex (const double x)
	gets nearest index More...
void	filter (const double absY=0.0, const double relY=0.0)
	executes filter More...
void	getPoints (std::vector< Point< double > > &points, const bool ySort, const bool desc)
	gets points array More...
bool	importData (boost::function< int(void *, int) > readFun)
	imports data More...
bool	exportData (boost::function< int(void *, int) > writeFun)
	exports data More...

Protected Member Functions
void	arrangePeaks ()
	arrange peaks
virtual bool	onLoadData (boost::function< int(void *, int) > readFun)
	loads data from file (override method) More...
virtual bool	onSaveData (boost::function< int(void *, int) > writeFun)
	saves data to file (override method) More...
virtual void	onClearPoints ()
	This method is called by clearPoints method. (override method)
virtual void	onAddPoint (const double x, const double y)
	This method is called by addPoint method. (override method) More...
virtual void	onInsertPoint (const unsigned int index, const double x, const double y)
	This method is called by insertPoint method. (override method) More...
virtual void	onDeletePoint (const unsigned int index)
	This method is called by deletePoint method. (override method) More...
virtual unsigned int	onGetLength ()
	this method is called by getLength method (override method) More...
virtual double	onGetX (const unsigned int index)
	This method is called by getX method. (override method) More...
virtual double	onGetY (const unsigned int index)
	This method is called by getY method. (override method) More...
virtual void	onReserve (const unsigned int num)
	This method is called by reserve method. (override method) More...
Protected Member Functions inherited from kome::core::XYData
void	updateRange ()
	updates range

Static Protected Member Functions
static bool	lessPeakX (PeakElement *p0, PeakElement *p1)
	compares to sort peaks by x coordinate More...
static bool	lessPeakY (PeakElement *p0, PeakElement *p1)
	compares to sort peaks by y coordinate More...

Protected Attributes
std::vector< PeakElement * >	m_peaks
std::string	m_title
std::vector< short >	m_charges
double	m_precursor
std::string	m_dataFile
Protected Attributes inherited from kome::core::XYData
bool	m_updated
double	m_minX
double	m_maxX
double	m_minY
double	m_maxY
unsigned long	m_version

Additional Inherited Members
Static Protected Attributes inherited from kome::core::XYData
static unsigned long	m_currentVersion = 0
	version More...

Detailed Description

peaks information class

Definition at line 35 of file Peaks.h.

Constructor & Destructor Documentation

kome::objects::Peaks::Peaks

(

const Peaks &

peaks

)

copy constructor

Parameters

[in]

peaks

copy source

Definition at line 45 of file Peaks.cpp.

                                 : kome::core::XYData( peaks ) {
    // initialize
    m_title = peaks.m_title;
    m_precursor = peaks.m_precursor;
    for( unsigned int i = 0; i < peaks.m_charges.size(); i++ ) {
        m_charges.push_back( peaks.m_charges[ i ] );
    }

// @date 2011.03.03 <Mod> M.Aihara ->
// soft cache DataPoints
#ifdef DATAPOINTS_SOFT_CACHE_TBB
    if(peaks.m_dps){
        m_dps = new kome::core::DataPoints( kome::core::DataPoints::FLOAT );
        *m_dps = *(peaks.m_dps);
    }else{
        m_dps = NULL;
    }
#endif // DATAPOINTS_SOFT_CACHE_TBB
// <Mod> M.Aihara <-

    m_title = peaks.m_title;
    m_charges = peaks.m_charges;
    m_precursor = peaks.m_precursor;
    m_dataFile = peaks.m_dataFile;

    // copy peaks
    if( peaks.m_peaks.size() == 0 ) {
        return;
    }

    m_peaks.reserve( peaks.m_peaks.size() );
    for( unsigned int i = 0; i < peaks.m_peaks.size(); i++ ) {
        // source peak
        PeakElement* src = peaks.m_peaks[ i ];

        // copy peak
        PeakElement* peak = new PeakElement( this );
        m_peaks.push_back( peak );

        peak->setX( src->getX() );
        peak->setY( src->getY() );
        peak->setLeft( src->getLeftX(), src->getLeftY() );
        peak->setRight( src->getRightX(), src->getRightY() );
        peak->setApex( src->getApexX(), src->getApexY() );
    }
}

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Member Function Documentation

void kome::objects::Peaks::addCharge

(

const short

charge

)

adds charge

Parameters

[in]

charge

charge

Definition at line 157 of file Peaks.cpp.

                                          {
    m_charges.push_back( charge );
}

PeakElement * kome::objects::Peaks::createPeak	(	const double	x,
		const double	y
	)

creates peak

Parameters

[in]	x	x element of peak
[in]	y	y element of peak

Returns

new peak object

Definition at line 353 of file Peaks.cpp.

                                                               {
    // add peak
    PeakElement* peak = new PeakElement( this, x, y );
    m_peaks.push_back( peak );

    // length
    unsigned int len = m_peaks.size();

    // set range
    if( x < m_minX || len == 0 ) {
        m_minX = x;
    }
    if( x > m_maxX || len == 0 ) {
        m_maxX = x;
    }
    if( y < m_minY || len == 0 ) {
        m_minY = y;
    }
    if( y > m_maxY || len == 0 ) {
        m_maxY = y;
    }

    m_updated = true;

    return peak;
}

short kome::objects::Peaks::getCharge

(

const unsigned int

index

)

gets charge

Parameters

[in]

index

charge index

Returns

charge

Definition at line 167 of file Peaks.cpp.

                                                 {
    // check index
    if( index >= m_charges.size() ) {
        LOG_WARN(
            FMT(
                "Charge index must be less than the number of charges. [%d/%d] ",
                index,
                m_charges.size()
            )
        );
        return 0;
    }

    return m_charges[ index ];
}

unsigned int kome::objects::Peaks::getNumberOfCharges

(

)

gets the number of charges

Returns

the number of charges

Definition at line 162 of file Peaks.cpp.

                                       {
    return m_charges.size();
}

PeakElement * kome::objects::Peaks::getPeak

(

const unsigned int

index

)

gets peak

Parameters

[in]

index

peak index

Returns

peak object (If NULL, the index is illegal.

Definition at line 381 of file Peaks.cpp.

                                                      {
    if( index >= m_peaks.size() ) {
        return NULL;
    }
    double x = getX( index );
    return m_peaks[ index ];
}

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PeakElement * kome::objects::Peaks::getPeakById

(

int

id

)

gets peak element by peak id

Parameters

[in]

id

peak id

Returns

peak element objects

Definition at line 587 of file Peaks.cpp.

                                       {
    arrangePeaks();

    for( unsigned int i=0; i < m_peaks.size(); i++ ){
        if( m_peaks[i]->getId() == id ){
            return m_peaks[i];
        }
    }
    return NULL;
}

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double kome::objects::Peaks::getPrecursor

(

)

gets precursor

Returns

precursor

Definition at line 189 of file Peaks.cpp.

                           {
    return m_precursor;
}

int kome::objects::Peaks::issueId

(

PeakElement *

peakElement

)

to issue the peak id

Parameters

[in]

peakElement

peak element objects

Returns

peak id

Definition at line 579 of file Peaks.cpp.

                                            {
    if( peakElement != NULL && peakElement->getId() > 0 ){
        return peakElement->getId()+1;
    }
    return 0;
}

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static bool kome::objects::Peaks::lessPeakX ( PeakElement *  p0, PeakElement *  p1  )

staticprotected

compares to sort peaks by x coordinate

Parameters

[in]	p0	peak to be compared
[in]	p1	peak to compare

Returns

If true, p0 sorts before p1.

Definition at line 569 of file Peaks.cpp.

                                                        {
    return ( p0->getX() < p1->getX() );
}

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static bool kome::objects::Peaks::lessPeakY ( PeakElement *  p0, PeakElement *  p1  )

staticprotected

compares to sort peaks by y coordinate

Parameters

[in]	p0	peak to be compared
[in]	p1	peak to compare

Returns

If true, p0 sorts before p1.

Definition at line 574 of file Peaks.cpp.

                                                        {
    return ( p0->getY() > p1->getY() );
}

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void kome::objects::Peaks::onAddPoint ( const double  x, const double  y  )

protectedvirtual

This method is called by addPoint method. (override method)

Parameters

[in]	x	x coordinate of point to be added
[in]	y	y coordinate of point to be added

Implements kome::core::XYData.

Definition at line 525 of file Peaks.cpp.

                                                       {
    createPeak( x, y );
}

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void kome::objects::Peaks::onDeletePoint ( const unsigned int  index )

protectedvirtual

This method is called by deletePoint method. (override method)

Parameters

[in]

index

point index

Implements kome::core::XYData.

Definition at line 540 of file Peaks.cpp.

                                                    {
    delete m_peaks[ index ];
    m_peaks.erase( m_peaks.begin() + index );
}

unsigned int kome::objects::Peaks::onGetLength ( )

protectedvirtual

this method is called by getLength method (override method)

Returns

the number of points

Implements kome::core::XYData.

Definition at line 546 of file Peaks.cpp.

                                {
    arrangePeaks();
    return m_peaks.size();
}

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double kome::objects::Peaks::onGetX ( const unsigned int  index )

protectedvirtual

This method is called by getX method. (override method)

Parameters

[in]

index

the index of point

Returns

x coordinate

Implements kome::core::XYData.

Definition at line 552 of file Peaks.cpp.

                                               {
    arrangePeaks();
    return m_peaks[ index ]->getX();
}

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double kome::objects::Peaks::onGetY ( const unsigned int  index )

protectedvirtual

This method is called by getY method. (override method)

Parameters

[in]

index

the index of point

Returns

y coordiante

Implements kome::core::XYData.

Definition at line 558 of file Peaks.cpp.

                                               {
    arrangePeaks();
    return m_peaks[ index ]->getY();
}

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void kome::objects::Peaks::onInsertPoint ( const unsigned int  index, const double  x, const double  y  )

protectedvirtual

This method is called by insertPoint method. (override method)

Parameters

[in]	index	insert position
[in]	x	x coordinate of point
[in]	y	y coordinate of point

Implements kome::core::XYData.

Definition at line 530 of file Peaks.cpp.

                                                                                    {
    // index
    int idx = std::min( (int)index, (int)m_peaks.size() );

    // insert
    PeakElement* peak = new PeakElement( this, x, y );
    m_peaks.insert( m_peaks.begin() + idx, peak );
}

bool kome::objects::Peaks::onLoadData ( boost::function< int(void *, int) >  readFun )

protectedvirtual

loads data from file (override method)

Parameters

[in]

readFun

read function

Returns

If true, it succeeded to load the data.

Reimplemented from kome::core::XYData.

Definition at line 429 of file Peaks.cpp.

                                                                    {
    // length
    unsigned long len = 0;
    readFun( &len, sizeof( len ) );

    // read data
    if( len > 0 ) {
        double* arr = new double[ len * 10 ];
        readFun( arr, sizeof( double ) * len * 10 );

        int* charges = new int[ len ];
        readFun( charges, sizeof( int ) * len );

        m_peaks.reserve( len );
        for( unsigned int i = 0; i < len; i++ ) {
            int idx = i * 10;
            double x  = arr[ idx + 0 ];
            double y  = arr[ idx + 1 ];
            double lx = arr[ idx + 2 ];
            double ly = arr[ idx + 3 ];
            double rx = arr[ idx + 4 ];
            double ry = arr[ idx + 5 ];
            double ax = arr[ idx + 6 ];
            double ay = arr[ idx + 7 ];
            double ar = arr[ idx + 8 ];
            double wi = arr[ idx + 9 ];
            int c = charges[ i ];

            PeakElement* peak = new PeakElement( this, x, y );
            peak->setLeft( lx, ly );
            peak->setRight( rx, ry );
            peak->setApex( ax, ay );
            peak->setArea( ar );
            peak->setFwhm( wi );
            peak->setCharge( c );

            m_peaks.push_back( peak );
        }

        delete[] arr;
        delete[] charges;
    }

    return true;
}

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void kome::objects::Peaks::onReserve ( const unsigned int  num )

protectedvirtual

This method is called by reserve method. (override method)

Parameters

[in]

num

of points to be reserved

Implements kome::core::XYData.

Definition at line 564 of file Peaks.cpp.

                                              {
    m_peaks.reserve( num );
}

bool kome::objects::Peaks::onSaveData ( boost::function< int(void *, int) >  writeFun )

protectedvirtual

saves data to file (override method)

Parameters

[in]

writeFun

write function

Returns

If true, it succeeded to save the data

Reimplemented from kome::core::XYData.

Definition at line 476 of file Peaks.cpp.

                                                                     {
    // length
    unsigned long len = m_peaks.size();
    writeFun( &len, sizeof( len ) );

    // write data
    if( len > 0 ) {
        double* arr = new double[ len * 10 ];

        for( unsigned int i = 0; i < len; i++ ) {
            // peak
            PeakElement* peak = m_peaks[ i ];

            // array
            int idx = i * 10;
            arr[ idx + 0 ] = peak->getX();
            arr[ idx + 1 ] = peak->getY();
            arr[ idx + 2 ] = peak->getLeftX();
            arr[ idx + 3 ] = peak->getLeftY();
            arr[ idx + 4 ] = peak->getRightX();
            arr[ idx + 5 ] = peak->getRightY();
            arr[ idx + 6 ] = ( peak->hasApex() ? peak->getApexX() : -1.0 );
            arr[ idx + 7 ] = ( peak->hasApex() ? peak->getApexY() : -1.0 );
            arr[ idx + 8 ] = ( peak->hasArea() ? peak->getArea() : -1.0 );
            arr[ idx + 9 ] = ( peak->hasFwhm() ? peak->getFwhm() : -1.0 );
        }

        writeFun( arr, sizeof( double ) * len * 10 );

        delete[] arr;

        // charges
        int* charges = new int[ len ];
        for( unsigned int i = 0; i < len; i++ ) {
            // peak
            PeakElement* peak = m_peaks[ i ];

            charges[ i ] = peak->getCharge();
        }

        writeFun( charges, sizeof( int ) * len );

        delete[] charges;
    }

    return true;
}

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Peaks & kome::objects::Peaks::operator=

(

const Peaks &

other

)

substitution operator

Parameters

[in]

other

source peaks object

Returns

copied peaks object

Definition at line 118 of file Peaks.cpp.

                                            {
    // initialize
    m_title = other.m_title;
    m_precursor = other.m_precursor;
    for( unsigned int i = 0; i < other.m_charges.size(); i++ ) {
        m_charges.push_back( other.m_charges[ i ] );
    }

    // clear points
    clearPoints();
    // copy peaks
    if( other.m_peaks.size() == 0 ) {
        return *this;
    }

    // add peaks
    reserve( other.m_peaks.size() );
    for( unsigned int i = 0; i < other.m_peaks.size(); i++ ) {
        // source peak
        PeakElement* src = other.m_peaks[ i ];

        // copy peak
        PeakElement* peak = createPeak( src->getX(), src->getY() );

        peak->setLeft( src->getLeftX(), src->getLeftY() );
        peak->setRight( src->getRightX(), src->getRightY() );
        peak->setApex( src->getApexX(), src->getApexY() );
        peak->setArea( src->getArea() );
    }

    return *this;
}

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void kome::objects::Peaks::setDataPoints

(

kome::core::XYData &

xyData

)

sets data points

Parameters

[in]

xyData

data points

Definition at line 301 of file Peaks.cpp.

                                                  {

    // manager
    kome::core::MsppManager& msppMgr = kome::core::MsppManager::getInstance();

    // init area
    for( unsigned int i = 0; i < m_peaks.size(); i++ ) {
        m_peaks[ i ]->setArea( -1.0 );
    }

    // delete previous data
    if( !m_dataFile.empty() ) {
        std::string oldDataPath = getpath( msppMgr.getTmpDir(), m_dataFile.c_str() );

        if( fileexists( oldDataPath.c_str() ) ) {
            removefile( oldDataPath.c_str() );
        }
    }

    // data file path
    static int tmpDirCnt = 0;

    std::string dir = getpath( "peaks_data", FMT( "%02x", tmpDirCnt ).c_str() );
    tmpDirCnt = ( tmpDirCnt + 1 ) % 0x100;

    std::string tmpFileName = msppMgr.getTmpFileName( "profile_data", ".xyd", dir.c_str() );
    m_dataFile = getpath( dir.c_str(), tmpFileName.c_str() );
    std::string tmpFilePath = getpath( msppMgr.getTmpDir(), m_dataFile.c_str() );

    // open file
    FILE* fp = fileopen( tmpFilePath.c_str(), "wb" );
    if( fp == NULL ) {
        m_dataFile.clear();
        return;
    }

    // copy data
    kome::core::DataPoints dps( kome::core::DataPoints::FLOAT );
    for( unsigned int i = 0; i < xyData.getLength(); i++ ) {
        dps.addPoint( xyData.getX( i ), xyData.getY( i ) );
    }

    // save data
    kome::core::FileAccessor acc( fp );
    dps.exportData( boost::bind( &kome::core::FileAccessor::write, &acc, _1, _2 ) );

    fclose( fp );
}

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void kome::objects::Peaks::setPrecursor

(

const double

precursor

)

sets precursor

Parameters

[in]

precursor

precursor

Definition at line 184 of file Peaks.cpp.

                                                 {
    m_precursor = precursor;
}

Member Data Documentation

std::vector< short > kome::objects::Peaks::m_charges

protected

charge array

Definition at line 73 of file Peaks.h.

std::string kome::objects::Peaks::m_dataFile

protected

data file

Definition at line 79 of file Peaks.h.

std::vector< PeakElement* > kome::objects::Peaks::m_peaks

protected

the array of peak elements

Definition at line 67 of file Peaks.h.

double kome::objects::Peaks::m_precursor

protected

precursor

Definition at line 76 of file Peaks.h.

std::string kome::objects::Peaks::m_title

protected

peak title

Definition at line 70 of file Peaks.h.

---

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

• DataObjects/Peaks.h
• DataObjects/Peaks.cpp