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 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... | |
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 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 | |
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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... | |
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 SimpleSearchEngine::main_().
void clearMSLevels | ( | ) |
clears the MS levels
Referenced by SimpleSearchEngine::main_().
bool containsMSLevel | ( | int | level | ) | const |
returns true
, if MS level level
has been set
Referenced by MzMLHandler< MapType >::handleCVParam_(), MzDataHandler< MapType >::startElement(), and MzXMLHandler< MapType >::startElement().
bool getAlwaysAppendData | ( | ) | const |
returns whether or not to always append the data to the given map (even if a consumer is given)
Referenced by MzMLHandler< MSExperiment<> >::populateChromatogramsWithData(), MzMLHandler< MSExperiment<> >::populateSpectraWithData(), and MzXMLHandler< MapType >::populateSpectraWithData_().
bool getCompression | ( | ) | const |
Referenced by MzMLHandler< MSExperiment<> >::writeBinaryDataArray().
bool getFillData | ( | ) | const |
returns whether to fill the actual data into the container (spectrum/chromatogram)
Referenced by MzXMLHandler< MapType >::characters(), MzMLHandler< MapType >::endElement(), MzMLHandler< MSExperiment<> >::populateChromatogramsWithData(), MzMLHandler< MSExperiment<> >::populateSpectraWithData(), and MzXMLHandler< MapType >::populateSpectraWithData_().
bool getIntensity32Bit | ( | ) | const |
Referenced by MzMLHandler< MSExperiment<> >::writeContainerData().
const DRange<1>& getIntensityRange | ( | ) | const |
Size getMaxDataPoolSize | ( | ) | const |
Get maximal size of the data pool.
Referenced by MzXMLHandler< MapType >::endElement(), MzMLHandler< MapType >::endElement(), and MzMLHandler< MSExperiment<> >::setOptions().
bool getMetadataOnly | ( | ) | const |
returns whether or not to load only meta data
Referenced by MzDataHandler< MapType >::startElement(), MzXMLHandler< MapType >::startElement(), and MzMLHandler< MapType >::startElement().
const std::vector<Int>& getMSLevels | ( | ) | const |
returns the set MS levels
bool getMz32Bit | ( | ) | const |
Referenced by MzMLHandler< MSExperiment<> >::writeContainerData().
const DRange<1>& getMZRange | ( | ) | const |
returns the MZ range
Referenced by MzXMLHandler< MapType >::doPopulateSpectraWithData_(), MzDataHandler< MapType >::fillData_(), DTA2DFile::load(), and MzMLHandler< MSExperiment<> >::populateSpectraWithData_().
MSNumpressCoder::NumpressConfig getNumpressConfigurationIntensity | ( | ) | const |
Set numpress configuration options for intensity dimension.
Referenced by MzMLHandler< MSExperiment<> >::writeBinaryDataArray().
MSNumpressCoder::NumpressConfig getNumpressConfigurationMassTime | ( | ) | const |
Set numpress configuration options for m/z or rt dimension.
Referenced by MzMLHandler< MSExperiment<> >::writeBinaryDataArray(), and MzMLHandler< MSExperiment<> >::writeContainerData().
const DRange<1>& getRTRange | ( | ) | const |
bool getSizeOnly | ( | ) | const |
returns whether or not to load only meta data
Referenced by MzMLHandler< MapType >::endElement(), and MzXMLHandler< MapType >::startElement().
bool getSkipXMLChecks | ( | ) | const |
returns whether to skip some XML checks and be fast instead
Referenced by MzMLHandler< MSExperiment<> >::populateChromatogramsWithData_(), and MzMLHandler< MSExperiment<> >::populateSpectraWithData_().
bool getSortChromatogramsByRT | ( | ) | const |
gets whether or not peaks in chromatograms should be sorted
Referenced by MzMLHandler< MSExperiment<> >::populateChromatogramsWithData().
bool getSortSpectraByMZ | ( | ) | const |
gets whether or not peaks in spectra should be sorted
Referenced by MzMLHandler< MSExperiment<> >::populateSpectraWithData(), and MzXMLHandler< MapType >::populateSpectraWithData_().
bool getWriteIndex | ( | ) | const |
Whether to write an index at the end of the file (e.g. indexedmzML file format)
Referenced by MzMLHandler< MapType >::writeHeader_().
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 >::doPopulateSpectraWithData_(), MzDataHandler< MapType >::fillData_(), DTA2DFile::load(), MzMLHandler< MSExperiment<> >::populateChromatogramsWithData_(), and MzMLHandler< MSExperiment<> >::populateSpectraWithData_().
bool hasMSLevels | ( | ) | const |
returns true
, if MS levels have been set
Referenced by MzMLHandler< MapType >::handleCVParam_(), MzDataHandler< MapType >::startElement(), and MzXMLHandler< MapType >::startElement().
bool hasMZRange | ( | ) | const |
returns true
if an MZ range has been set
Referenced by MzXMLHandler< MapType >::doPopulateSpectraWithData_(), MzDataHandler< MapType >::fillData_(), DTA2DFile::load(), and MzMLHandler< MSExperiment<> >::populateSpectraWithData_().
bool hasRTRange | ( | ) | const |
returns true
if an RT range has been set
Referenced by MzDataHandler< MapType >::cvParam_(), MzMLHandler< MapType >::handleCVParam_(), DTA2DFile::load(), MzMLHandler< MSExperiment<> >::populateChromatogramsWithData_(), and MzXMLHandler< MapType >::startElement().
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(), SwathFile::populateMetaData_(), MzXMLFile::transform(), and MzMLFile::transform().
void setCompression | ( | bool | compress | ) |
void setFillData | ( | bool | only | ) |
sets whether to fill the actual data into the container (spectrum/chromatogram)
Referenced by OnDiscMSExperiment< PeakT, ChromatogramPeakT >::loadMetaData_(), SwathFile::loadMzXML(), and SwathFile::populateMetaData_().
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(), MzXMLFile::transformFirstPass_(), and MzMLFile::transformFirstPass_().
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 setNumpressConfigurationIntensity | ( | MSNumpressCoder::NumpressConfig | config | ) |
Get numpress configuration options for intensity dimension.
void setNumpressConfigurationMassTime | ( | MSNumpressCoder::NumpressConfig | config | ) |
Get numpress configuration options for m/z or rt dimension.
void setRTRange | ( | const DRange< 1 > & | range | ) |
restricts the range of RT values for peaks to load
void setSizeOnly | ( | bool | only | ) |
Referenced by MzXMLFile::transformFirstPass_(), and MzMLFile::transformFirstPass_().
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)
void setWriteSupplementalData | ( | bool | write | ) |
sets whether or not to write supplemental peak data in MzData files
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OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 12:49:29 using doxygen 1.8.11 |