PeakFileOptions Class Reference

Options for loading files containing peak data. More...

#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>

List of all members.

Public Member Functions
	PeakFileOptions ()
	Default constructor.
	~PeakFileOptions ()
	Destructor.
Meta data option
void	setMetadataOnly (bool only)
	sets whether or not to load only meta data
bool	getMetadataOnly () const
	returns whether or not to load only meta data
Suplemental data option
void	setWriteSupplementalData (bool write)
	sets whether or not to write supplemental peak data in MzData files
bool	getWriteSupplementalData () const
	returns whether or not to write supplemental peak data in MzData files
RT range option
void	setRTRange (const DRange< 1 > &range)
	restricts the range of RT values for peaks to load
bool	hasRTRange () const
	returns true if an RT range has been set
const DRange< 1 > &	getRTRange () const
	returns the RT range
m/z range option
void	setMZRange (const DRange< 1 > &range)
	restricts the range of MZ values for peaks to load
bool	hasMZRange () const
	returns true if an MZ range has been set
const DRange< 1 > &	getMZRange () const
	returns the MZ range
Intensity range option
void	setIntensityRange (const DRange< 1 > &range)
	restricts the range of intensity values for peaks to load
bool	hasIntensityRange () const
	returns true if an intensity range has been set
const DRange< 1 > &	getIntensityRange () const
	returns the intensity range
MS levels option
With this option, MS level filters can be set. Note: The original spectrum identifiers are stored as the nativeID of the spectrum.
void	setMSLevels (const std::vector< Int > &levels)
	sets the desired MS levels for peaks to load
void	addMSLevel (int level)
	adds a desired MS level for peaks to load
void	clearMSLevels ()
	clears the MS levels
bool	hasMSLevels () const
	returns true, if MS levels have been set
bool	containsMSLevel (int level) const
	returns true, if MS level level has been set
const std::vector< Int > &	getMSLevels () const
	returns the set MS levels
Compression options
Note: This option is ignored if the format does not support compression
void	setCompression (bool compress)
bool	getCompression () const
Precision options
Note: This option is ignored if the format does not support multiple precisions
void	setMz32Bit (bool mz_32_bit)
bool	getMz32Bit () const
void	setIntensity32Bit (bool int_32_bit)
bool	getIntensity32Bit () const
Private Attributes
bool	metadata_only_
bool	write_supplemental_data_
bool	has_rt_range_
bool	has_mz_range_
bool	has_intensity_range_
bool	mz_32_bit_
bool	int_32_bit_
DRange< 1 >	rt_range_
DRange< 1 >	mz_range_
DRange< 1 >	intensity_range_
std::vector< Int >	ms_levels_
bool	zlib_compression_

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Detailed Description

Options for loading files containing peak data.

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Constructor & Destructor Documentation

PeakFileOptions

(

)

Default constructor.

~PeakFileOptions

(

)

Destructor.

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Member Function Documentation

void addMSLevel

(

int

level

)

adds a desired MS level for peaks to load

void clearMSLevels

(

)

clears the MS levels

bool containsMSLevel

(

int

level

)

const

returns true, if MS level level has been set

Referenced by MzMLHandler< MapType >::handleCVParam_(), MzXMLHandler< MapType >::startElement(), and MzDataHandler< MapType >::startElement().

bool getCompression

(

)

const

Referenced by MzMLHandler< MapType >::writeTo().

bool getIntensity32Bit

(

)

const

Referenced by MzMLHandler< MapType >::writeTo().

const DRange<1>& getIntensityRange

(

)

const

returns the intensity range

Referenced by MzXMLHandler< MapType >::endElement(), MzMLHandler< MapType >::fillChromatogramData_(), MzMLHandler< MapType >::fillData_(), MzDataHandler< MapType >::fillData_(), and DBAdapter::loadSpectrum().

bool getMetadataOnly

(

)

const

returns whether or not to load only meta data

Referenced by DBAdapter::loadExperiment(), MzXMLHandler< MapType >::startElement(), MzMLHandler< MapType >::startElement(), and MzDataHandler< MapType >::startElement().

const std::vector<Int>& getMSLevels

(

)

const

returns the set MS levels

Referenced by DBAdapter::loadExperiment().

bool getMz32Bit

(

)

const

Referenced by MzMLHandler< MapType >::writeTo().

const DRange<1>& getMZRange

(

)

const

returns the MZ range

Referenced by MzXMLHandler< MapType >::endElement(), MzMLHandler< MapType >::fillData_(), MzDataHandler< MapType >::fillData_(), and DBAdapter::loadSpectrum().

const DRange<1>& getRTRange

(

)

const

returns the RT range

Referenced by MzDataHandler< MapType >::cvParam_(), MzMLHandler< MapType >::fillChromatogramData_(), MzMLHandler< MapType >::handleCVParam_(), DBAdapter::loadExperiment(), and MzXMLHandler< MapType >::startElement().

bool getWriteSupplementalData

(

)

const

returns whether or not to write supplemental peak data in MzData files

Referenced by MzDataHandler< MapType >::writeTo().

bool hasIntensityRange

(

)

const

returns true if an intensity range has been set

Referenced by MzXMLHandler< MapType >::endElement(), MzMLHandler< MapType >::fillChromatogramData_(), MzMLHandler< MapType >::fillData_(), MzDataHandler< MapType >::fillData_(), and DBAdapter::loadSpectrum().

bool hasMSLevels

(

)

const

returns true, if MS levels have been set

Referenced by MzMLHandler< MapType >::handleCVParam_(), DBAdapter::loadExperiment(), MzXMLHandler< MapType >::startElement(), and MzDataHandler< MapType >::startElement().

bool hasMZRange

(

)

const

returns true if an MZ range has been set

Referenced by MzXMLHandler< MapType >::endElement(), MzMLHandler< MapType >::fillData_(), MzDataHandler< MapType >::fillData_(), and DBAdapter::loadSpectrum().

bool hasRTRange

(

)

const

returns true if an RT range has been set

Referenced by MzDataHandler< MapType >::cvParam_(), MzMLHandler< MapType >::fillChromatogramData_(), MzMLHandler< MapType >::handleCVParam_(), DBAdapter::loadExperiment(), and MzXMLHandler< MapType >::startElement().

void setCompression

(

bool

compress

)

void setIntensity32Bit

(

bool

int_32_bit

)

void setIntensityRange

(

const DRange< 1 > &

range

)

restricts the range of intensity values for peaks to load

void setMetadataOnly

(

bool

only

)

sets whether or not to load only meta data

Referenced by TOPPViewBase::metadataDatabaseDialog(), and TOPPViewBase::metadataFileDialog().

void setMSLevels

(

const std::vector< Int > &

levels

)

sets the desired MS levels for peaks to load

void setMz32Bit

(

bool

mz_32_bit

)

void setMZRange

(

const DRange< 1 > &

range

)

restricts the range of MZ values for peaks to load

void setRTRange

(

const DRange< 1 > &

range

)

restricts the range of RT values for peaks to load

void setWriteSupplementalData

(

bool

write

)

sets whether or not to write supplemental peak data in MzData files

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Member Data Documentation

bool has_intensity_range_ [private]

bool has_mz_range_ [private]

bool has_rt_range_ [private]

bool int_32_bit_ [private]

DRange<1> intensity_range_ [private]

bool metadata_only_ [private]

std::vector<Int> ms_levels_ [private]

bool mz_32_bit_ [private]

DRange<1> mz_range_ [private]

DRange<1> rt_range_ [private]

bool write_supplemental_data_ [private]

bool zlib_compression_ [private]