#include <ManipulatedSample.h>

Inheritance diagram for kome::operation::ManipulatedSample:

Collaboration diagram for kome::operation::ManipulatedSample:

Public Member Functions
	ManipulatedSample (kome::objects::Sample &org)
	constructor

virtual	~ManipulatedSample ()
	destructor

void	addOperation (kome::objects::XYDataOperation *opt)
	add operation More...

void	removeOperation (kome::objects::XYDataOperation *opt)
	remove operation More...

void	clearOperation ()
	clear operation

kome::objects::Sample *	getOrgSample ()
	gets original sample More...

void	setOperationInfo (kome::plugin::PluginCall call, kome::objects::SettingParameterValues settings, kome::objects::DataGroupNode *stdGroup)
	set operation info More...

unsigned int	getNumberOfOperation ()
	get number of operation More...

kome::objects::XYDataOperation *	getOperation (int index)
	get operation More...

Public Member Functions inherited from kome::objects::Sample
	Sample (SampleSet *sampleSet)
	constructor

virtual	~Sample ()
	destructor

SampleSet *	getSampleSet ()
	gets sample set object More...

void	setSampleIndex (const int index)
	sets sample index More...

int	getSampleIndex ()
	gets sample index More...

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

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

void	setType (const char *type)
	sets sample type More...

const char *	getType ()
	gets sample type More...

void	setInstrument (const char *instrument)
	sets instrument name More...

const char *	getInstrument ()
	gets instrument name More...

void	setMsCompany (const char *company)
	sets MS company More...

const char *	getMsCompany ()
	gets MS company More...

void	setSoftwareName (const char *name)
	sets software name More...

const char *	getSoftwareName ()
	gets software name More...

void	setSoftwareVersion (const char *version)
	sets software version More...

const char *	getSoftwareVersion ()
	gets software version More...

void	setOpened (const bool opened)
	sets opened flag More...

bool	isOpened ()
	judges whther this sample is opened or not More...

void	setEdited (const bool edited)
	sets edited flag More...

bool	isEdited ()
	judges whther this sample is edited or not More...

DataGroupNode *	getRootDataGroupNode ()
	gets root spectrum group More...

DataSet *	getHiddenDataSet ()
	gets the hidden data set More...

unsigned int	getNumberOfGroups ()
	gets the number of spectrum groups More...

DataGroupNode *	getGroup (const unsigned int index)
	gets spectrum group More...

void	setParallelReadable (const bool readable)
	sets parallel readable or not More...

bool	isParallelReadable ()
	gets whether this sample is parallel readable or not More...

bool	openSample (kome::core::Progress *progress=NULL)
	opens sample [out] progress progressbar to display More...

bool	closeSample ()
	closes sample More...

void	detectPeaksByAPI (Spectrum spec, Peaks peaks)
	detect peaks using Application Progreamming Interface More...

void	setSampleId (int id)
	set sample id More...

int	getSampleId ()
	get sample id More...

int	issueSpecId ()
	to issue the spectrum id More...

Spectrum *	getSpectrumById (int id)
	A spectrum is acquired by id. More...

int	issueChromId (Sample *sample)
	to issue the chromatogram id More...

Chromatogram *	getChromatogramById (int id)
	A schromatogram is acquired by id. More...

int	issueGroupId (Sample *sample)
	to issue the group id More...

DataGroupNode *	getGroupById (int id)
	A DataGroupNode is qcquired by id. More...

bool	isSupportedAPIPeaks ()
	judges whether API peak detection is supported on this sample. More...

void	setSupportedAPIPeaks (const bool supported)
	sets API peak dtection is supported on this sample. More...

Protected Member Functions
void	addSpectrum (kome::objects::DataGroupNode orgGroup, kome::objects::DataGroupNode dstGroup)
	add spectrum More...

virtual bool	onOpenSample (kome::objects::DataGroupNode rootGroup, kome::core::Progress progress=NULL)
	This method is called by openSample method. (abstract method) More...

virtual bool	onCloseSample ()
	This method is called by closeSample method. (abstract method) More...

Protected Member Functions inherited from kome::objects::Sample
void	getGroups (DataGroupNode *parentGroup=NULL)
	gets spectrum groups More...

virtual void	onDetectPeaksByAPI (Spectrum spec, Peaks peaks)
	This methos is called by detectPeakByAPI method.

Protected Attributes
kome::objects::Sample &	m_org

std::vector < kome::objects::XYDataOperation * >	m_opts

Protected Attributes inherited from kome::objects::Sample
SampleSet *	m_sampleSet

int	m_sampleIdx

int	m_specId

std::string	m_name

std::string	m_type

std::string	m_instrument

std::string	m_company

std::string	m_softwareName

std::string	m_softwareVersion

DataGroupNode *	m_root

bool	m_opened

bool	m_edited

std::vector< DataGroupNode * >	m_groups

bool	m_parallelReadable

DataSet	m_hiddenSet

bool	m_supportedApiPeaks

Additional Inherited Members
Static Public Member Functions inherited from kome::objects::Sample
static void	resetId ()
	Reset the ID of the sample.

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

static int	issueSampleId ()
	to issue the sample id More...

static Sample *	getSampleById (int id)
	A sample is acquired by id. More...

Static Protected Attributes inherited from kome::objects::Sample
static int	m_optSampleId = 0

static std::vector< std::string >	m_commonProps

Detailed Description

ManipulatedSample class.

Definition at line 25 of file ManipulatedSample.h.

Member Function Documentation

void kome::operation::ManipulatedSample::addOperation ( kome::objects::XYDataOperation * opt )

add operation

Parameters

opt	xyData Operaiton object

Definition at line 95 of file ManipulatedSample.cpp.

                                                                    {
     bool bflg = false;
     for( unsigned int i=0; i < m_opts.size(); i++ ){
         if( opt == m_opts[i] ){
             bflg = true;
             break;
         }
     }
     if( bflg ){
         m_opts.push_back( opt );
     }
 }

void kome::operation::ManipulatedSample::addSpectrum	(	kome::objects::DataGroupNode *	orgGroup,
		kome::objects::DataGroupNode *	dstGroup
	)

protected

add spectrum

Parameters

orgGroup	group of original sample data
dstGroup	group of manipulated sample data

Definition at line 68 of file ManipulatedSample.cpp.

                                                                                                            {    
     if( orgGroup != NULL && dstGroup != NULL ){
         // creating spectra
         for( unsigned int i=0; i < orgGroup->getNumberOfSpectra(); i++ ){           
             kome::operation::ManipulatedSpectrum* spec = new kome::operation::ManipulatedSpectrum( this, *orgGroup->getSpectrum(i) );
             dstGroup->addSpectrum( spec );
             spec->setSample( this );
         }
 
         // creating chromatograms
         for( unsigned int i = 0; i < orgGroup->getNumberOfChromatograms(); i++ ) {
             kome::objects::Chromatogram* orgChrom = orgGroup->getChromatogram( i );
             TransformedChromatogram* chrom = new TransformedChromatogram( *orgChrom, false );
             dstGroup->addChromatogram( chrom );
         }
 
         // child groups
         for( unsigned int i = 0; i < orgGroup->getNumberOfChildren(); i++ ) {
             kome::objects::DataGroupNode* orgChild = orgGroup->getChild( i );
             kome::objects::DataGroupNode* dstChild = dstGroup->createChildGroup( orgChild->getName() );
 
             addSpectrum( orgChild, dstChild );
         }
     }   
 }

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unsigned int kome::operation::ManipulatedSample::getNumberOfOperation ( )

get number of operation

Returns: operation size

Definition at line 160 of file ManipulatedSample.cpp.

                                                     {
     return m_opts.size();
 }

kome::objects::XYDataOperation * kome::operation::ManipulatedSample::getOperation ( int index )

get operation

Returns: xyData Operation

Definition at line 165 of file ManipulatedSample.cpp.

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

kome::objects::Sample * kome::operation::ManipulatedSample::getOrgSample ( )

gets original sample

Returns: org sample object

Definition at line 155 of file ManipulatedSample.cpp.

                                                   {
     return &m_org;
 }

bool kome::operation::ManipulatedSample::onCloseSample ( )

protectedvirtual

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

Returns: If true, it succeeded to close this sample.

Implements kome::objects::Sample.

Definition at line 143 of file ManipulatedSample.cpp.

                                      {
     if( m_root != NULL ){
         delete m_root;
     }
     m_root = NULL;
     
     clearOperation();
 
     return true;
 }

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bool kome::operation::ManipulatedSample::onOpenSample	(	kome::objects::DataGroupNode *	rootGroup,
		kome::core::Progress *	progress = `NULL`
	)

protectedvirtual

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

Parameters

[out]	rootGroup	root spectrum group
[out]	progress	progress bar instance

Returns: If true, it succeeded to open this sample.

Implements kome::objects::Sample.

Definition at line 138 of file ManipulatedSample.cpp.

                                                                                                      {
     return true;
 }

void kome::operation::ManipulatedSample::removeOperation ( kome::objects::XYDataOperation * opt )

remove operation

Parameters

opt	xyData Operation object

Definition at line 109 of file ManipulatedSample.cpp.

                                                                         {
     
     for( unsigned int i=0; i < m_opts.size(); i++ ){
         if( opt == m_opts[i] ){
             delete m_opts[i];
             m_opts.erase( m_opts.begin() + i );
             return;
         }
     }
 }

void kome::operation::ManipulatedSample::setOperationInfo	(	kome::plugin::PluginCall *	call,
		kome::objects::SettingParameterValues *	settings,
		kome::objects::DataGroupNode *	stdGroup
	)

set operation info

Parameters

call	plugin call
settings	setting parameter values
stdGroup	standard group

Definition at line 129 of file ManipulatedSample.cpp.

                                                                                                                                                      {
     // create filter subtract object
     Normalization* normaliz = new Normalization();
     
     normaliz->setNormalizInfo( call, settings, stdGroup );
     m_opts.push_back( (kome::objects::XYDataOperation*)normaliz );
 }

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Member Data Documentation

std::vector<kome::objects::XYDataOperation*> kome::operation::ManipulatedSample::m_opts

protected

operations

Definition at line 44 of file ManipulatedSample.h.

kome::objects::Sample& kome::operation::ManipulatedSample::m_org

protected

orignal sample

Definition at line 41 of file ManipulatedSample.h.

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

DataOperation/ManipulatedSample.h
DataOperation/ManipulatedSample.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

Member Data Documentation