OpenMS
2.6.0
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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... | |
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.
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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 | |
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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.
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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 () |
do these options skip spectra or chromatograms due to RT or MSLevel filters? More... | |
Options for loading files containing peak data.
PeakFileOptions | ( | ) |
Default constructor.
PeakFileOptions | ( | const PeakFileOptions & | ) |
Copy constructor.
~PeakFileOptions | ( | ) |
Destructor.
void addMSLevel | ( | int | level | ) |
adds a desired MS level for peaks to load
Referenced by NucleicAcidSearchEngine::main_().
void clearMSLevels | ( | ) |
clears the MS levels
Referenced by NucleicAcidSearchEngine::main_().
bool containsMSLevel | ( | int | level | ) | const |
returns true
, if MS level level
has been set
bool getAlwaysAppendData | ( | ) | const |
returns whether or not to always append the data to the given map (even if a consumer is given)
bool getCompression | ( | ) | const |
bool getFillData | ( | ) | const |
returns whether to fill the actual data into the container (spectrum/chromatogram)
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)
bool getForceTPPCompatability | ( | ) | const |
[mzML only!] Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z
bool getIntensity32Bit | ( | ) | const |
const DRange<1>& getIntensityRange | ( | ) | const |
returns the intensity range
Referenced by DTA2DFile::load().
Size getMaxDataPoolSize | ( | ) | const |
Get maximal size of the data pool.
bool getMetadataOnly | ( | ) | const |
returns whether or not to load only meta data
const std::vector<Int>& getMSLevels | ( | ) | const |
returns the set MS levels
bool getMz32Bit | ( | ) | const |
const DRange<1>& getMZRange | ( | ) | const |
returns the MZ range
Referenced by DTA2DFile::load().
MSNumpressCoder::NumpressConfig getNumpressConfigurationFloatDataArray | ( | ) | const |
Set numpress configuration options for float data arrays.
MSNumpressCoder::NumpressConfig getNumpressConfigurationIntensity | ( | ) | const |
Set numpress configuration options for intensity dimension.
MSNumpressCoder::NumpressConfig getNumpressConfigurationMassTime | ( | ) | const |
Set numpress configuration options for m/z or rt dimension.
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)
const DRange<1>& getRTRange | ( | ) | const |
returns the RT range
Referenced by DTA2DFile::load().
bool getSkipXMLChecks | ( | ) | const |
returns whether to skip some XML checks and be fast instead
bool getSortChromatogramsByRT | ( | ) | const |
gets whether or not peaks in chromatograms should be sorted
bool getSortSpectraByMZ | ( | ) | const |
gets whether or not peaks in spectra should be sorted
bool getWriteIndex | ( | ) | const |
Whether to write an index at the end of the file (e.g. indexedmzML file format)
bool getWriteSupplementalData | ( | ) | const |
returns whether or not to write supplemental peak data in MzData files
bool hasFilters | ( | ) |
do these options skip spectra or chromatograms due to RT or MSLevel filters?
bool hasIntensityRange | ( | ) | const |
returns true
if an intensity range has been set
Referenced by DTA2DFile::load().
bool hasMSLevels | ( | ) | const |
returns true
, if MS levels have been set
bool hasMZRange | ( | ) | const |
returns true
if an MZ range has been set
Referenced by DTA2DFile::load().
bool hasRTRange | ( | ) | const |
returns true
if an RT range has been set
Referenced by DTA2DFile::load().
void setAlwaysAppendData | ( | bool | only | ) |
void setCompression | ( | bool | compress | ) |
Referenced by TOPPOpenSwathBase::prepareChromOutput().
void setFillData | ( | bool | only | ) |
sets whether to fill the actual data into the container (spectrum/chromatogram)
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)
void setForceTPPCompatability | ( | bool | forceTPP | ) |
[mzML only!] Whether to skip writing the <isolationWindow> tag so that TPP finds the correct precursor m/z
void setIntensity32Bit | ( | bool | int_32_bit | ) |
void setIntensityRange | ( | const DRange< 1 > & | range | ) |
restricts the range of intensity values for peaks to load
void setMaxDataPoolSize | ( | Size | size | ) |
Set maximal size of the data pool.
void setMetadataOnly | ( | bool | only | ) |
sets whether or not to load only meta data
Referenced by 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 setNumpressConfigurationFloatDataArray | ( | MSNumpressCoder::NumpressConfig | config | ) |
Get numpress configuration options for float data arrays.
void setNumpressConfigurationIntensity | ( | MSNumpressCoder::NumpressConfig | config | ) |
Get numpress configuration options for intensity dimension.
Referenced by TOPPOpenSwathBase::prepareChromOutput().
void setNumpressConfigurationMassTime | ( | MSNumpressCoder::NumpressConfig | config | ) |
Get numpress configuration options for m/z or rt dimension.
Referenced by TOPPOpenSwathBase::prepareChromOutput().
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)
void setRTRange | ( | const DRange< 1 > & | range | ) |
restricts the range of RT values for peaks to load
void setSkipXMLChecks | ( | bool | only | ) |
sets whether to skip some XML checks and be fast instead
void setSortChromatogramsByRT | ( | bool | sort | ) |
sets whether or not to sort peaks in chromatograms
void setSortSpectraByMZ | ( | bool | sort | ) |
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().
void setWriteSupplementalData | ( | bool | write | ) |
sets whether or not to write supplemental peak data in MzData files
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