Configuration class for mz5 im- and export. More...

#include <Configuration_mz5.hpp>

Public Types
enum	SpectrumLoadPolicy { SLP_InitializeAllOnCreation, SLP_InitializeAllOnFirstCall }
	Enumeration for different load strategies for spectra. More...
enum	ChromatogramLoadPolicy { CLP_InitializeAllOnCreation, CLP_InitializeAllOnFirstCall }
enum	MZ5DataSets { ControlledVocabulary, FileContent, Contact, CVReference, CVParam, UserParam, RefParam, ParamGroups, SourceFiles, Samples, Software, ScanSetting, InstrumentConfiguration, DataProcessing, Run, SpectrumMetaData, SpectrumBinaryMetaData, SpectrumIndex, SpectrumMZ, SpectrumIntensity, ChromatogramMetaData, ChromatogramBinaryMetaData, ChromatogramIndex, ChomatogramTime, ChromatogramIntensity, FileInformation }
	Enumeration to simplify the use of datasets. More...

Public Member Functions
	Configuration_mz5 ()
	Default constructor.
	Configuration_mz5 (const Configuration_mz5 &)
	Copy constructor.
	Configuration_mz5 (const pwiz::msdata::MSDataFile::WriteConfig &config)
	Conversion constructor for WriteConfig objects.
Configuration_mz5 &	operator= (const Configuration_mz5 &rhs)
	Assign operator.
const std::string &	getNameFor (const MZ5DataSets v)
	Returns dataset name for a requested dataset.
MZ5DataSets	getVariableFor (const std::string &name)
	Returns dataset enumeration value for a given string.
const H5::DataType &	getDataTypeFor (const MZ5DataSets v)
	Returns dataset type.
const hsize_t &	getChunkSizeFor (const MZ5DataSets v)
	Returns chunk size for a dataset.
const size_t &	getBufferSizeFor (const MZ5DataSets v)
	Returns buffer size for a dataset.
const size_t &	getBufferInMb ()
	Returns mz5 cache in Mb.
const size_t	getBufferInB ()
	Returns mz5 cache in byte.
const size_t &	getRdccSlots ()
	Returns number of used rdcc slots.
const SpectrumLoadPolicy &	getSpectrumLoadPolicy () const
	Getter for spectrum load policy.
const ChromatogramLoadPolicy &	getChromatogramLoadPolicy () const
	Getter for chromatogram load policy.
const bool	doTranslating () const
	Getter for translation flag.
void	setTranslating (const bool flag) const
	Setter for translation flag.
const int	getDeflateLvl ()
	Getter for compression level.
const bool	doShuffel ()
	Getter for shuffle flag.

Static Public Attributes
static unsigned short	MZ5_FILE_MAJOR_VERSION
static unsigned short	MZ5_FILE_MINOR_VERSION
static bool	PRINT_HDF5_EXCEPTIONS
static hsize_t	EMPTY_CHUNK_SIZE
	Value for empty chunk size.
static size_t	NO_BUFFER_SIZE
	Default value to use no buffer.

Private Member Functions
void	init (const bool deltamz, const bool translateinten)
	Initializes configuration object.

Private Attributes
pwiz::msdata::MSDataFile::WriteConfig	config_
	Internal copy of pwiz configuration object.
std::map< MZ5DataSets, std::string >	variableNames_
	Map which holds the translation of datasets to dataset names.
std::map< std::string, MZ5DataSets >	variableVariables_
	Map which holds the translation of dataset names to datasets.
std::map< MZ5DataSets, H5::DataType >	variableTypes_
	Map which holds the data types for a dataset.
std::map< MZ5DataSets, hsize_t >	variableChunkSizes_
	Map which holds the chunk size for a dataset.
std::map< MZ5DataSets, size_t >	variableBufferSizes_
	Map which holds the buffer size for a dataset.
size_t	bufferInMB_
	MZ5 cache in MB.
size_t	rdccSolts_
	Number of rdcc slots.
SpectrumLoadPolicy	spectrumLoadPolicy_
	Spectrum load policy.
ChromatogramLoadPolicy	chromatogramLoadPolicy_
	Chromaogram load policy.
bool	doTranslating_
	flag for translation.
int	deflateLvl_
	Compression level.

Detailed Description

Configuration class for mz5 im- and export.

This class is holding several different configuration options, such as dataset names, dataset types and different buffering and chunking values.

Definition at line 39 of file Configuration_mz5.hpp.

Member Enumeration Documentation

enum pwiz::msdata::mz5::Configuration_mz5::SpectrumLoadPolicy

Enumeration for different load strategies for spectra.

Enumerator:

SLP_InitializeAllOnCreation	Initializes all meta information of all spectra at the creation a an spectrum list obeject.
SLP_InitializeAllOnFirstCall	Initialzes all meta information of all spectra at the first getSpectrum() call.

Definition at line 50 of file Configuration_mz5.hpp.

    {
        /**
         * Initializes all meta information of all spectra at the creation a an spectrum list obeject.
         */
        SLP_InitializeAllOnCreation,
        /**
         * Initialzes all meta information of all spectra at the first getSpectrum() call.
         */
        SLP_InitializeAllOnFirstCall
    //SLP_PreemptionMode not implemented yet
    //SLP_OnDemand not implemented yet
    //SLP_CachedOnDemand not implemented yet
    };

enum pwiz::msdata::mz5::Configuration_mz5::ChromatogramLoadPolicy

Enumerator:

CLP_InitializeAllOnCreation	Initialize and keep all chromatograms when initializing the chromatogram list.
CLP_InitializeAllOnFirstCall	Initialize and keep all chromatograms when requesting the first chromatogram.

Definition at line 65 of file Configuration_mz5.hpp.

                                {
        /**
         * Initialize and keep all chromatograms when initializing the chromatogram list.
         */
        CLP_InitializeAllOnCreation,
        /**
         * Initialize and keep all chromatograms when requesting the first chromatogram.
         */
        CLP_InitializeAllOnFirstCall
    //CLP_PreemptionMode not implemented yet
    //CLP_OnDemand not implemented yet
    //CLP_CachedOnDemand not implemented yet
    };

enum pwiz::msdata::mz5::Configuration_mz5::MZ5DataSets

Enumeration to simplify the use of datasets.

These values are used to determine dataset specific parameters, such as chunk size, buffer size, name and type.

Enumerator:

ControlledVocabulary	Dataset for the controlled vocabulary sets.
FileContent	File content dataset.
Contact	Dataset containing contact infomation.
CVReference	Dataset containing all used controlled vocabulary accessions (prefix, accession, definition).
CVParam	Dataset containing all controlled vocabulary parameters.
UserParam	Dataset containing all user parameters.
RefParam	Dataset containing all referenced parameter groups.
ParamGroups	Dataset for parameter groups.
SourceFiles	Source file dataset.
Samples	Sample datatset.
Software	Software dataset.
ScanSetting	Scan setting datatset.
InstrumentConfiguration	Instrument configuration datatset.
DataProcessing	Data processing dataset.
Run	Dataset containing all meta information for all runs.
SpectrumMetaData	Dataset containing all meta information of all spectra.
SpectrumBinaryMetaData	Dataset containing all meta information of all binary data elements for spectra.
SpectrumIndex	Index dataset. kth element points to the end of the kth spectrum in MZ and SIntensity.
SpectrumMZ	Dataset containing all mz values for all spectra.
SpectrumIntensity	Dataset containing all intensity values for all spectra.
ChromatogramMetaData	Dataset containing all meta information of all chromatograms.
ChromatogramBinaryMetaData	Dataset containing all meta information of all binary data elements for chromatograms.
ChromatogramIndex	Index dataset. kth element points to the end of the kth chromatogram in Time and CIntensity.
ChomatogramTime	Dataset containing all time values.
ChromatogramIntensity	Dataset containing all chromatogram intensities.
FileInformation	Dataset containing information about the file and specific dataset configurations.

Definition at line 82 of file Configuration_mz5.hpp.

    {
        /**
         * Dataset for the controlled vocabulary sets.
         */
        ControlledVocabulary,
        /**
         * File content dataset.
         */
        FileContent,
        /**
         * Dataset containing contact infomation.
         */
        Contact,
        /**
         * Dataset containing all used controlled vocabulary accessions (prefix, accession, definition).
         */
        CVReference,
        /**
         * Dataset containing all controlled vocabulary parameters.
         */
        CVParam,
        /**
         * Dataset containing all user parameters.
         */
        UserParam,
        /**
         * Dataset containing all referenced parameter groups.
         */
        RefParam,
        /**
         * Dataset for parameter groups.
         */
        ParamGroups,
        /**
         * Source file dataset.
         */
        SourceFiles,
        /**
         * Sample datatset.
         */
        Samples,
        /**
         * Software dataset.
         */
        Software,
        /**
         * Scan setting datatset.
         */
        ScanSetting,
        /**
         * Instrument configuration datatset.
         */
        InstrumentConfiguration,
        /**
         * Data processing dataset.
         */
        DataProcessing,
        /**
         * Dataset containing all meta information for all runs.
         */
        Run,
        /**
         * Dataset containing all meta information of all spectra.
         */
        SpectrumMetaData,
        /**
         * Dataset containing all meta information of all binary data elements for spectra.
         */
        SpectrumBinaryMetaData,
        /**
         * Index dataset. kth element points to the end of the kth spectrum in MZ and SIntensity.
         */
        SpectrumIndex,
        /**
         * Dataset containing all mz values for all spectra.
         */
        SpectrumMZ,
        /**
         * Dataset containing all intensity values for all spectra.
         */
        SpectrumIntensity,
        /**
         * Dataset containing all meta information of all chromatograms.
         */
        ChromatogramMetaData,
        /**
         * Dataset containing all meta information of all binary data elements for chromatograms.
         */
        ChromatogramBinaryMetaData,
        /**
         * Index dataset. kth element points to the end of the kth chromatogram in Time and CIntensity.
         */
        ChromatogramIndex,
        /**
         * Dataset containing all time values.
         */
        ChomatogramTime,
        /**
         * Dataset containing all chromatogram intensities.
         */
        ChromatogramIntensity,
        /**
         * Dataset containing information about the file and specific dataset configurations.
         */
        FileInformation
    };

Constructor & Destructor Documentation

pwiz::msdata::mz5::Configuration_mz5::Configuration_mz5 ( )

Default constructor.

Initializes default parameters.

pwiz::msdata::mz5::Configuration_mz5::Configuration_mz5 ( const Configuration_mz5 & )

Copy constructor.

pwiz::msdata::mz5::Configuration_mz5::Configuration_mz5 ( const pwiz::msdata::MSDataFile::WriteConfig & config )

Conversion constructor for WriteConfig objects.

Uses values in config to set up specific options such as compression or precision.

Parameters:

config a pwiz config object

Member Function Documentation

Configuration_mz5& pwiz::msdata::mz5::Configuration_mz5::operator= ( const Configuration_mz5 & rhs )

Assign operator.

Parameters:

rhs	right hand side of assign operator.

Returns:: the altered object

const std::string& pwiz::msdata::mz5::Configuration_mz5::getNameFor ( const MZ5DataSets v )

Returns dataset name for a requested dataset.

Parameters:

v dataset

Returns:: dataset name

MZ5DataSets pwiz::msdata::mz5::Configuration_mz5::getVariableFor ( const std::string & name )

Returns dataset enumeration value for a given string.

Returns out_of_range if string does not exist.

Parameters:

name	dataset name

Returns:: dataset enumeration value

const H5::DataType& pwiz::msdata::mz5::Configuration_mz5::getDataTypeFor ( const MZ5DataSets v )

Returns dataset type.

Parameters:

v dataset

Returns:: mz5 data type reference

const hsize_t& pwiz::msdata::mz5::Configuration_mz5::getChunkSizeFor ( const MZ5DataSets v )

Returns chunk size for a dataset.

Parameters:

v dataset

Returns:: chunk size. EMPTY_CHUNK_SIZE if no chunking should be used.

const size_t& pwiz::msdata::mz5::Configuration_mz5::getBufferSizeFor ( const MZ5DataSets v )

Returns buffer size for a dataset.

Buffers are mainly used to speed up writing of mz and spectrum intensities.

Parameters:

v dataset

Returns:: buffer size. NO_BUFFER_SIZE if no buffer will be used.

const size_t& pwiz::msdata::mz5::Configuration_mz5::getBufferInMb ( )

Returns mz5 cache in Mb.

The mz5 cache is used for chunked datasets. This effects the random read time.

Returns:: mz5 cache size

const size_t pwiz::msdata::mz5::Configuration_mz5::getBufferInB ( )

Returns mz5 cache in byte.

See getBufferInMb()

Returns:: mz5 cache in byte

const size_t& pwiz::msdata::mz5::Configuration_mz5::getRdccSlots ( )

Returns number of used rdcc slots.

This is currently constant 41957L, but should be the the next prime after 10-100 times the number of chunks fitting into the cache.

Returns:: number of rdcc slots

const SpectrumLoadPolicy& pwiz::msdata::mz5::Configuration_mz5::getSpectrumLoadPolicy ( ) const

Getter for spectrum load policy.

Returns:: spectrum load policy

const ChromatogramLoadPolicy& pwiz::msdata::mz5::Configuration_mz5::getChromatogramLoadPolicy ( ) const

Getter for chromatogram load policy.

Returns:: spectrum load policy

const bool pwiz::msdata::mz5::Configuration_mz5::doTranslating ( ) const

Getter for translation flag.

If this flag is set, mz values of mass spectra are saved as delta mz's. This greatly improves compression rate and significantly reduces file size.

Returns:: true of tranlating is enabled, otherwise false.

void pwiz::msdata::mz5::Configuration_mz5::setTranslating ( const bool flag ) const

Setter for translation flag.

Parameters:

flag	true of translation of mz and intensity values is be enabled;

const int pwiz::msdata::mz5::Configuration_mz5::getDeflateLvl ( )

Getter for compression level.

Default is 1 if compression is enabled, since the gain in compression rate of >2 is negligible.

Returns:: value between 0-9(0=no compression, 1=fast compression, 9=high compression)

const bool pwiz::msdata::mz5::Configuration_mz5::doShuffel ( )

Getter for shuffle flag.

Shuffle greatly increases compression rate.

Returns:: true if shuffel is enabled, otherwise false.

void pwiz::msdata::mz5::Configuration_mz5::init	(	const bool	deltamz,
		const bool	translateinten
	)

private

Initializes configuration object.

Member Data Documentation

unsigned short pwiz::msdata::mz5::Configuration_mz5::MZ5_FILE_MAJOR_VERSION

static

Definition at line 43 of file Configuration_mz5.hpp.

unsigned short pwiz::msdata::mz5::Configuration_mz5::MZ5_FILE_MINOR_VERSION

static

Definition at line 44 of file Configuration_mz5.hpp.

bool pwiz::msdata::mz5::Configuration_mz5::PRINT_HDF5_EXCEPTIONS

static

Definition at line 45 of file Configuration_mz5.hpp.

hsize_t pwiz::msdata::mz5::Configuration_mz5::EMPTY_CHUNK_SIZE

static

Value for empty chunk size.

Should be 0.

Definition at line 314 of file Configuration_mz5.hpp.

size_t pwiz::msdata::mz5::Configuration_mz5::NO_BUFFER_SIZE

static

Default value to use no buffer.

Should be 0.

Definition at line 318 of file Configuration_mz5.hpp.

pwiz::msdata::MSDataFile::WriteConfig pwiz::msdata::mz5::Configuration_mz5::config_

mutableprivate

Internal copy of pwiz configuration object.

Definition at line 329 of file Configuration_mz5.hpp.

std::map<MZ5DataSets, std::string> pwiz::msdata::mz5::Configuration_mz5::variableNames_

private

Map which holds the translation of datasets to dataset names.

Definition at line 333 of file Configuration_mz5.hpp.

std::map<std::string, MZ5DataSets> pwiz::msdata::mz5::Configuration_mz5::variableVariables_

private

Map which holds the translation of dataset names to datasets.

Definition at line 337 of file Configuration_mz5.hpp.

std::map<MZ5DataSets, H5::DataType> pwiz::msdata::mz5::Configuration_mz5::variableTypes_

private

Map which holds the data types for a dataset.

Definition at line 341 of file Configuration_mz5.hpp.

std::map<MZ5DataSets, hsize_t> pwiz::msdata::mz5::Configuration_mz5::variableChunkSizes_

private

Map which holds the chunk size for a dataset.

Definition at line 345 of file Configuration_mz5.hpp.

std::map<MZ5DataSets, size_t> pwiz::msdata::mz5::Configuration_mz5::variableBufferSizes_

private

Map which holds the buffer size for a dataset.

Definition at line 349 of file Configuration_mz5.hpp.

size_t pwiz::msdata::mz5::Configuration_mz5::bufferInMB_

private

MZ5 cache in MB.

Definition at line 353 of file Configuration_mz5.hpp.

size_t pwiz::msdata::mz5::Configuration_mz5::rdccSolts_

private

Number of rdcc slots.

Definition at line 357 of file Configuration_mz5.hpp.

SpectrumLoadPolicy pwiz::msdata::mz5::Configuration_mz5::spectrumLoadPolicy_

private

Spectrum load policy.

Definition at line 361 of file Configuration_mz5.hpp.

ChromatogramLoadPolicy pwiz::msdata::mz5::Configuration_mz5::chromatogramLoadPolicy_

private

Chromaogram load policy.

Definition at line 365 of file Configuration_mz5.hpp.

bool pwiz::msdata::mz5::Configuration_mz5::doTranslating_

mutableprivate

flag for translation.

Definition at line 369 of file Configuration_mz5.hpp.

int pwiz::msdata::mz5::Configuration_mz5::deflateLvl_

private

Compression level.

If compression level is > 0, shuffle is enable by default.

Definition at line 373 of file Configuration_mz5.hpp.

The documentation for this class was generated from the following file:

/Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/msdata/mz5/Configuration_mz5.hpp

Public Types

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation