PeakFileOptions Class Reference

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

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

Collaboration diagram for PeakFileOptions:

Public Member Functions
	PeakFileOptions ()
	Default constructor. More...
	PeakFileOptions (const PeakFileOptions &)
	Copy constructor. More...
PeakFileOptions &	operator= (const PeakFileOptions &)=default
	Copy assignment. More...
	~PeakFileOptions ()
	Destructor. 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
	returns true, if data should be compressed when writing More...
lazyload option
sets whether or not to always append the data to the given map (even if a consumer is given)
void	setAlwaysAppendData (bool only)
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
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...
MSNumpressCoder::NumpressConfig	getNumpressConfigurationFloatDataArray () const
	Set numpress configuration options for float data arrays. More...
void	setNumpressConfigurationFloatDataArray (MSNumpressCoder::NumpressConfig config)
	Get numpress configuration options for float data arrays. More...

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.
bool	metadata_only_
bool	force_maxquant_compatibility_
	for mzXML-writing only: set a fixed vendor (Thermo Scientific), mass analyzer (FTMS) More...
bool	force_tpp_compatibility_
	for mzML-writing only: work around some bugs in TPP file parsers More...
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	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_
MSNumpressCoder::NumpressConfig	np_config_fda_
Size	maximal_data_pool_size_
bool	precursor_mz_selected_ion_
Size	getMaxDataPoolSize () const
	Get maximal size of the data pool. More...
void	setMaxDataPoolSize (Size size)
	Set maximal size of the data pool. More...
bool	getPrecursorMZSelectedIon () const
	[mzML only!] Whether to use the "selected ion m/z" value as the precursor m/z value (alternative: use the "isolation window target m/z" value) More...
void	setPrecursorMZSelectedIon (bool choice)
	[mzML only!] Set whether to use the "selected ion m/z" value as the precursor m/z value (alternative: use the "isolation window target m/z" value) More...
bool	hasFilters () const
	do these options skip spectra or chromatograms due to RT or MSLevel filters? More...

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 NucleicAcidSearchEngine::main_().

clearMSLevels()

void clearMSLevels

(

)

clears the MS levels

Referenced by NucleicAcidSearchEngine::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

returns true, if data should be compressed when writing

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().

getNumpressConfigurationFloatDataArray()

MSNumpressCoder::NumpressConfig getNumpressConfigurationFloatDataArray

(

)

const

Set numpress configuration options for float data arrays.

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.

getPrecursorMZSelectedIon()

bool getPrecursorMZSelectedIon

(

)

const

[mzML only!] Whether to use the "selected ion m/z" value as the precursor m/z value (alternative: use the "isolation window target m/z" value)

getRTRange()

const DRange<1>& getRTRange

(

)

const

returns the RT range

Referenced by DTA2DFile::load().

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

hasFilters()

bool hasFilters

(

)

const

do these options skip spectra or chromatograms due to RT or MSLevel filters?

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().

operator=()

PeakFileOptions& operator= ( const PeakFileOptions &  )

default

Copy assignment.

setAlwaysAppendData()

void setAlwaysAppendData

(

bool

only

)

setCompression()

void setCompression

(

bool

compress

)

Referenced by MzMLSwathFileConsumer::addNewSwathMap_(), and TOPPOpenSwathBase::prepareChromOutput().

setFillData()

void setFillData

(

bool

only

)

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

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)

setForceTPPCompatability()

void setForceTPPCompatability

(

bool

forceTPP

)

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

setIntensity32Bit()

void setIntensity32Bit

(

bool

int_32_bit

)

setIntensityRange()

void setIntensityRange

(

const DRange< 1 > &

range

)

restricts the range of intensity values for peaks to load

Referenced by TOPPFLASHDeconv::main_().

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

setMz32Bit()

void setMz32Bit

(

bool

mz_32_bit

)

setMZRange()

void setMZRange

(

const DRange< 1 > &

range

)

restricts the range of MZ values for peaks to load

Referenced by TOPPFLASHDeconv::main_().

setNumpressConfigurationFloatDataArray()

void setNumpressConfigurationFloatDataArray

(

MSNumpressCoder::NumpressConfig

config

)

Get numpress configuration options for float data arrays.

setNumpressConfigurationIntensity()

void setNumpressConfigurationIntensity

(

MSNumpressCoder::NumpressConfig

config

)

Get numpress configuration options for intensity dimension.

Referenced by TOPPOpenSwathBase::prepareChromOutput().

setNumpressConfigurationMassTime()

void setNumpressConfigurationMassTime

(

MSNumpressCoder::NumpressConfig

config

)

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

Referenced by TOPPOpenSwathBase::prepareChromOutput().

setPrecursorMZSelectedIon()

void setPrecursorMZSelectedIon

(

bool

choice

)

[mzML only!] Set whether to use the "selected ion m/z" value as the precursor m/z value (alternative: use the "isolation window target m/z" value)

setRTRange()

void setRTRange

(

const DRange< 1 > &

range

)

restricts the range of RT values for peaks to load

Referenced by TOPPFLASHDeconv::main_().

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 TOPPOpenSwathBase::prepareChromOutput().

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

for mzXML-writing only: set a fixed vendor (Thermo Scientific), mass analyzer (FTMS)

force_tpp_compatibility_

bool force_tpp_compatibility_

private

for mzML-writing only: work around some bugs in TPP file parsers

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_fda_

MSNumpressCoder::NumpressConfig np_config_fda_

private

np_config_int_

MSNumpressCoder::NumpressConfig np_config_int_

private

np_config_mz_

MSNumpressCoder::NumpressConfig np_config_mz_

private

precursor_mz_selected_ion_

bool precursor_mz_selected_ion_

private

rt_range_

DRange<1> rt_range_

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