PeakFileOptions Class Reference

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

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

Public Member Functions
	PeakFileOptions ()
	Default constructor. More...
	PeakFileOptions (const PeakFileOptions &)
	Copy constructor. More...
	~PeakFileOptions ()
	Destructor. More...
bool	getWriteIndex () const
	Whether to write an index at the end of the file (e.g. indexedmzML file format) More...
void	setWriteIndex (bool write_index)
	Whether to write an index at the end of the file (e.g. indexedmzML file format) More...
MSNumpressCoder::NumpressConfig	getNumpressConfigurationMassTime () const
	Set numpress configuration options for m/z or rt dimension. More...
void	setNumpressConfigurationMassTime (MSNumpressCoder::NumpressConfig config)
	Get numpress configuration options for m/z or rt dimension. More...
MSNumpressCoder::NumpressConfig	getNumpressConfigurationIntensity () const
	Set numpress configuration options for intensity dimension. More...
void	setNumpressConfigurationIntensity (MSNumpressCoder::NumpressConfig config)
	Get numpress configuration options for intensity dimension. More...
Meta data and file format option
void	setMetadataOnly (bool only)
	sets whether or not to load only meta data More...
bool	getMetadataOnly () const
	returns whether or not to load only meta data More...
void	setForceMQCompatability (bool forceMQ)
	[mzXML only!] Whether to write a scan-index and meta data to indicate a Thermo FTMS/ITMS instrument (required to have parameter control in MQ) More...
bool	getForceMQCompatability () const
	[mzXML only!] Whether to write a scan-index and meta data to indicate a Thermo FTMS/ITMS instrument (required to have parameter control in MQ) More...
void	setForceTPPCompatability (bool forceTPP)
	[mzML only!] Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z More...
bool	getForceTPPCompatability () const
	[mzML only!] Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z More...
Supplemental data option
void	setWriteSupplementalData (bool write)
	sets whether or not to write supplemental peak data in MzData files More...
bool	getWriteSupplementalData () const
	returns whether or not to write supplemental peak data in MzData files More...
RT range option
void	setRTRange (const DRange< 1 > &range)
	restricts the range of RT values for peaks to load More...
bool	hasRTRange () const
	returns true if an RT range has been set More...
const DRange< 1 > &	getRTRange () const
	returns the RT range More...
m/z range option
void	setMZRange (const DRange< 1 > &range)
	restricts the range of MZ values for peaks to load More...
bool	hasMZRange () const
	returns true if an MZ range has been set More...
const DRange< 1 > &	getMZRange () const
	returns the MZ range More...
Intensity range option
void	setIntensityRange (const DRange< 1 > &range)
	restricts the range of intensity values for peaks to load More...
bool	hasIntensityRange () const
	returns true if an intensity range has been set More...
const DRange< 1 > &	getIntensityRange () const
	returns the intensity range More...
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 More...
void	addMSLevel (int level)
	adds a desired MS level for peaks to load More...
void	clearMSLevels ()
	clears the MS levels More...
bool	hasMSLevels () const
	returns true, if MS levels have been set More...
bool	containsMSLevel (int level) const
	returns true, if MS level level has been set More...
const std::vector< Int > &	getMSLevels () const
	returns the set MS levels More...
Compression options
Note This option is ignored if the format does not support compression
void	setCompression (bool compress)
bool	getCompression () const
lazyload option
sets whether or not to load only the count
void	setSizeOnly (bool only)
bool	getSizeOnly () const
	returns whether or not to load only meta data More...
void	setAlwaysAppendData (bool only)
	sets whether or not to always append the data to the given map (even if a consumer is given) More...
bool	getAlwaysAppendData () const
	returns whether or not to always append the data to the given map (even if a consumer is given) More...
void	setFillData (bool only)
	sets whether to fill the actual data into the container (spectrum/chromatogram) More...
bool	getFillData () const
	returns whether to fill the actual data into the container (spectrum/chromatogram) More...
void	setSkipXMLChecks (bool only)
	sets whether to skip some XML checks and be fast instead More...
bool	getSkipXMLChecks () const
	returns whether to skip some XML checks and be fast instead More...
sort peaks in spectra / chromatograms by position
sets whether or not to sort peaks in spectra
void	setSortSpectraByMZ (bool sort)
bool	getSortSpectraByMZ () const
	gets whether or not peaks in spectra should be sorted More...
void	setSortChromatogramsByRT (bool sort)
	sets whether or not to sort peaks in chromatograms More...
bool	getSortChromatogramsByRT () const
	gets whether or not peaks in chromatograms should be sorted More...
Precision options
Note that m/z and RT are controlled with the same flag (for spectra and chromatograms) while there is a separate flag for intensity. 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
Data pool size options
Some file readers and writers can process the data in parallel by reading in parts of the file and keeping it in memory and then process this partial data in parallel. This parameter specifies how many data points (spectra/chromatograms) should be read before parallel processing is initiated.
Size	getMaxDataPoolSize () const
	Get maximal size of the data pool. More...
void	setMaxDataPoolSize (Size size)
	Set maximal size of the data pool. More...

Private Attributes
bool	metadata_only_
bool	force_maxquant_compatibility_
bool	force_tpp_compatibility_
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_
bool	size_only_
bool	always_append_data_
bool	skip_xml_checks_
bool	sort_spectra_by_mz_
bool	sort_chromatograms_by_rt_
bool	fill_data_
bool	write_index_
MSNumpressCoder::NumpressConfig	np_config_mz_
MSNumpressCoder::NumpressConfig	np_config_int_
Size	maximal_data_pool_size_

Detailed Description

Options for loading files containing peak data.

Constructor & Destructor Documentation

PeakFileOptions() [1/2]

PeakFileOptions

(

)

Default constructor.

PeakFileOptions() [2/2]

PeakFileOptions

(

const PeakFileOptions &

)

Copy constructor.

~PeakFileOptions()

~PeakFileOptions

(

)

Destructor.

Member Function Documentation

addMSLevel()

void addMSLevel

(

int

level

)

adds a desired MS level for peaks to load

Referenced by TOPPOpenPepXLLF::main_(), SimpleSearchEngine::main_(), TOPPOpenPepXL::main_(), and RNPxlSearch::main_().

clearMSLevels()

void clearMSLevels

(

)

clears the MS levels

Referenced by TOPPOpenPepXLLF::main_(), SimpleSearchEngine::main_(), TOPPOpenPepXL::main_(), and RNPxlSearch::main_().

containsMSLevel()

bool containsMSLevel

(

int

level

)

const

returns true, if MS level level has been set

getAlwaysAppendData()

bool getAlwaysAppendData

(

)

const

returns whether or not to always append the data to the given map (even if a consumer is given)

getCompression()

bool getCompression

(

)

const

getFillData()

bool getFillData

(

)

const

returns whether to fill the actual data into the container (spectrum/chromatogram)

getForceMQCompatability()

bool getForceMQCompatability

(

)

const

[mzXML only!] Whether to write a scan-index and meta data to indicate a Thermo FTMS/ITMS instrument (required to have parameter control in MQ)

getForceTPPCompatability()

bool getForceTPPCompatability

(

)

const

[mzML only!] Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z

getIntensity32Bit()

bool getIntensity32Bit

(

)

const

getIntensityRange()

const DRange<1>& getIntensityRange

(

)

const

returns the intensity range

Referenced by DTA2DFile::load().

getMaxDataPoolSize()

Size getMaxDataPoolSize

(

)

const

Get maximal size of the data pool.

getMetadataOnly()

bool getMetadataOnly

(

)

const

returns whether or not to load only meta data

getMSLevels()

const std::vector<Int>& getMSLevels

(

)

const

returns the set MS levels

getMz32Bit()

bool getMz32Bit

(

)

const

getMZRange()

const DRange<1>& getMZRange

(

)

const

returns the MZ range

Referenced by DTA2DFile::load().

getNumpressConfigurationIntensity()

MSNumpressCoder::NumpressConfig getNumpressConfigurationIntensity

(

)

const

Set numpress configuration options for intensity dimension.

getNumpressConfigurationMassTime()

MSNumpressCoder::NumpressConfig getNumpressConfigurationMassTime

(

)

const

Set numpress configuration options for m/z or rt dimension.

getRTRange()

const DRange<1>& getRTRange

(

)

const

returns the RT range

Referenced by DTA2DFile::load().

getSizeOnly()

bool getSizeOnly

(

)

const

returns whether or not to load only meta data

getSkipXMLChecks()

bool getSkipXMLChecks

(

)

const

returns whether to skip some XML checks and be fast instead

getSortChromatogramsByRT()

bool getSortChromatogramsByRT

(

)

const

gets whether or not peaks in chromatograms should be sorted

getSortSpectraByMZ()

bool getSortSpectraByMZ

(

)

const

gets whether or not peaks in spectra should be sorted

getWriteIndex()

bool getWriteIndex

(

)

const

Whether to write an index at the end of the file (e.g. indexedmzML file format)

getWriteSupplementalData()

bool getWriteSupplementalData

(

)

const

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

hasIntensityRange()

bool hasIntensityRange

(

)

const

returns true if an intensity range has been set

Referenced by DTA2DFile::load().

hasMSLevels()

bool hasMSLevels

(

)

const

returns true, if MS levels have been set

hasMZRange()

bool hasMZRange

(

)

const

returns true if an MZ range has been set

Referenced by DTA2DFile::load().

hasRTRange()

bool hasRTRange

(

)

const

returns true if an RT range has been set

Referenced by DTA2DFile::load().

setAlwaysAppendData()

void setAlwaysAppendData

(

bool

only

)

sets whether or not to always append the data to the given map (even if a consumer is given)

Referenced by SwathFile::loadMzXML(), and SwathFile::populateMetaData_().

setCompression()

void setCompression

(

bool

compress

)

Referenced by extractCachedMetaFilename(), and SortPairDoubleByFirst().

setFillData()

void setFillData

(

bool

only

)

sets whether to fill the actual data into the container (spectrum/chromatogram)

Referenced by OnDiscMSExperiment::loadMetaData_(), SwathFile::loadMzXML(), and SwathFile::populateMetaData_().

setForceMQCompatability()

void setForceMQCompatability

(

bool

forceMQ

)

[mzXML only!] Whether to write a scan-index and meta data to indicate a Thermo FTMS/ITMS instrument (required to have parameter control in MQ)

Referenced by extractCachedMetaFilename().

setForceTPPCompatability()

void setForceTPPCompatability

(

bool

forceTPP

)

[mzML only!] Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z

Referenced by extractCachedMetaFilename().

setIntensity32Bit()

void setIntensity32Bit

(

bool

int_32_bit

)

setIntensityRange()

void setIntensityRange

(

const DRange< 1 > &

range

)

restricts the range of intensity values for peaks to load

setMaxDataPoolSize()

void setMaxDataPoolSize

(

Size

size

)

Set maximal size of the data pool.

setMetadataOnly()

void setMetadataOnly

(

bool

only

)

sets whether or not to load only meta data

Referenced by TOPPViewBase::metadataFileDialog().

setMSLevels()

void setMSLevels

(

const std::vector< Int > &

levels

)

sets the desired MS levels for peaks to load

Referenced by TOPPMetaProSIP::main_().

setMz32Bit()

void setMz32Bit

(

bool

mz_32_bit

)

setMZRange()

void setMZRange

(

const DRange< 1 > &

range

)

restricts the range of MZ values for peaks to load

setNumpressConfigurationIntensity()

void setNumpressConfigurationIntensity

(

MSNumpressCoder::NumpressConfig

config

)

Get numpress configuration options for intensity dimension.

Referenced by extractCachedMetaFilename(), and SortPairDoubleByFirst().

setNumpressConfigurationMassTime()

void setNumpressConfigurationMassTime

(

MSNumpressCoder::NumpressConfig

config

)

Get numpress configuration options for m/z or rt dimension.

Referenced by extractCachedMetaFilename(), and SortPairDoubleByFirst().

setRTRange()

void setRTRange

(

const DRange< 1 > &

range

)

restricts the range of RT values for peaks to load

setSizeOnly()

void setSizeOnly

(

bool

only

)

setSkipXMLChecks()

void setSkipXMLChecks

(

bool

only

)

sets whether to skip some XML checks and be fast instead

setSortChromatogramsByRT()

void setSortChromatogramsByRT

(

bool

sort

)

sets whether or not to sort peaks in chromatograms

setSortSpectraByMZ()

void setSortSpectraByMZ

(

bool

sort

)

setWriteIndex()

void setWriteIndex

(

bool

write_index

)

Whether to write an index at the end of the file (e.g. indexedmzML file format)

Referenced by extractCachedMetaFilename(), and SortPairDoubleByFirst().

setWriteSupplementalData()

void setWriteSupplementalData

(

bool

write

)

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

Member Data Documentation

always_append_data_

bool always_append_data_

private

fill_data_

bool fill_data_

private

force_maxquant_compatibility_

bool force_maxquant_compatibility_

private

force_tpp_compatibility_

bool force_tpp_compatibility_

private

has_intensity_range_

bool has_intensity_range_

private

has_mz_range_

bool has_mz_range_

private

has_rt_range_

bool has_rt_range_

private

int_32_bit_

bool int_32_bit_

private

intensity_range_

DRange<1> intensity_range_

private

maximal_data_pool_size_

Size maximal_data_pool_size_

private

metadata_only_

bool metadata_only_

private

ms_levels_

std::vector<Int> ms_levels_

private

mz_32_bit_

bool mz_32_bit_

private

mz_range_

DRange<1> mz_range_

private

np_config_int_

MSNumpressCoder::NumpressConfig np_config_int_

private

np_config_mz_

MSNumpressCoder::NumpressConfig np_config_mz_

private

rt_range_

DRange<1> rt_range_

private

size_only_

bool size_only_

private

skip_xml_checks_

bool skip_xml_checks_

private

sort_chromatograms_by_rt_

bool sort_chromatograms_by_rt_

private

sort_spectra_by_mz_

bool sort_spectra_by_mz_

private

write_index_

bool write_index_

private

write_supplemental_data_

bool write_supplemental_data_

private

zlib_compression_

bool zlib_compression_

private