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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 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.

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...
 
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
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 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< Intms_levels_
 
bool zlib_compression_
 
bool size_only_
 
bool always_append_data_
 
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

Default constructor.

Copy constructor.

Destructor.

Member Function Documentation

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

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
bool getFillData ( ) const
bool getIntensity32Bit ( ) const
const DRange<1>& getIntensityRange ( ) const
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
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

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)

bool getWriteSupplementalData ( ) const

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

bool hasIntensityRange ( ) const
bool hasMSLevels ( ) const

returns true, if MS levels have been set

bool hasMZRange ( ) const
bool hasRTRange ( ) const

returns true if an RT range has been set

Referenced by DTA2DFile::load(), and MzMLHandler< MSExperiment<> >::populateChromatogramsWithData_().

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 SwathFile::loadMzXML(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::openFile(), 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)
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

Member Data Documentation

bool always_append_data_
private
bool fill_data_
private
bool has_intensity_range_
private
bool has_mz_range_
private
bool has_rt_range_
private
bool int_32_bit_
private
DRange<1> intensity_range_
private
Size maximal_data_pool_size_
private
bool metadata_only_
private
std::vector<Int> ms_levels_
private
bool mz_32_bit_
private
DRange<1> mz_range_
private
MSNumpressCoder::NumpressConfig np_config_int_
private
MSNumpressCoder::NumpressConfig np_config_mz_
private
DRange<1> rt_range_
private
bool size_only_
private
bool sort_chromatograms_by_rt_
private
bool sort_spectra_by_mz_
private
bool write_index_
private
bool write_supplemental_data_
private
bool zlib_compression_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:42 using doxygen 1.8.9.1