| OpenMS 2.5.0

Public Member Functions | Private Attributes | List of all members
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...
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...
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 ()
| do these options skip spectra or chromatograms due to RT or MSLevel filters? 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 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
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_
| 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_

## 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

## ◆ 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 | ( |  | ) |

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().

## ◆ setAlwaysAppendData()

void setAlwaysAppendData | ( | bool | only | ) |

## ◆ setCompression()

void setCompression | ( | bool | compress | ) |

Referenced by 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

## ◆ 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

## ◆ 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

## ◆ 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