This class is used for reading and writing information to a mz5 file. More...

#include <Connection_mz5.hpp>

Public Types
enum	OpenPolicy { FailIfFileExists, RemoveAndCreate, ReadWrite, ReadOnly }
	mz5 file open policy. More...

Public Member Functions
	Connection_mz5 (const std::string filename, const OpenPolicy op=ReadOnly, const Configuration_mz5 config=Configuration_mz5())
	Default constructor.
	~Connection_mz5 ()
	Closes all open datasets and flushes file to filesystem.
void	createAndWrite1DDataSet (hsize_t size, void *data, const Configuration_mz5::MZ5DataSets v)
	Creates and write a one dimensional dataset.
void	extendData (const std::vector< double > &d1, const Configuration_mz5::MZ5DataSets v)
	Extends data of to a dataset.
const std::map < Configuration_mz5::MZ5DataSets, size_t > &	getFields ()
	Returns a list of all existing datasets in this file.
void *	readDataSet (Configuration_mz5::MZ5DataSets v, size_t &dsend, void *ptr=0)
	Reads a dataset.
void	clean (const Configuration_mz5::MZ5DataSets v, void *data, const size_t dsend)
	Clean up of open datasets and destruction of corresponding data elements.
void	getData (std::vector< double > &data, const Configuration_mz5::MZ5DataSets v, const hsize_t start, const hsize_t end)
	Gets data from a numerical dataset and writes it to the vector.
const Configuration_mz5 &	getConfiguration ()
	Getter.

Private Member Functions
H5::DSetCreatPropList	getCParm (int rank, const Configuration_mz5::MZ5DataSets &v, const hsize_t &datadim)
	Creates a DSetCreatPropList for a dataset.
H5::DataSet	getDataSet (int rank, hsize_t dim, hsize_t maxdim, const Configuration_mz5::MZ5DataSets v)
	Creates a dataset.
void	readFile ()
	Initializes a file and read internal mz5 information.
void	extendAndWrite1DDataSet (const H5::DataSet &dataset, const std::vector< double > &d1)
	Extends and appends data to an existing dataset with no buffer.
void	addToBuffer (std::vector< double > &b, const std::vector< double > &d1, const size_t bs, const H5::DataSet &dataset)
	Internal method to add data to a buffer.
void	flush (const Configuration_mz5::MZ5DataSets v)
	Flushes all data to the hard drive.
void	close ()
	Closes the file and flushes all open buffers/datasets.

Private Attributes
std::map < Configuration_mz5::MZ5DataSets, size_t >	fields_
	Existing field in file.
H5::H5File *	file_
	MZ5 file reference.
Configuration_mz5	config_
	mz5 configuration object.
std::map < Configuration_mz5::MZ5DataSets, H5::DataSet >	bufferMap_
	Mapping from a dataset enumeration value to the dataset.
std::map < Configuration_mz5::MZ5DataSets, std::vector< double > >	buffers_
	Mapping from a dataset enumeration value to a buffer.
bool	closed_
	Flag whether file is closed or not.

Detailed Description

This class is used for reading and writing information to a mz5 file.

On destruction it will automatically close all existing datasets and flush the file.

Definition at line 40 of file Connection_mz5.hpp.

Member Enumeration Documentation

enum pwiz::msdata::mz5::Connection_mz5::OpenPolicy

mz5 file open policy.

Enumerator:

FailIfFileExists	Fails if the file already exists.
RemoveAndCreate	If file exists, it will be deleted and created empty.
ReadWrite	Open file with read and write support.
ReadOnly	Open file with read only support.

Definition at line 46 of file Connection_mz5.hpp.

    {
        /**
         * Fails if the file already exists.
         */
        FailIfFileExists,
        /**
         * If file exists, it will be deleted and created empty.
         */
        RemoveAndCreate,
        /**
         * Open file with read and write support.
         */
        ReadWrite,
        /**
         * Open file with read only support.
         */
        ReadOnly
    };

Constructor & Destructor Documentation

pwiz::msdata::mz5::Connection_mz5::Connection_mz5	(	const std::string	filename,
		const OpenPolicy	op = `ReadOnly`,
		const Configuration_mz5	config = `Configuration_mz5()`
	)

Default constructor.

When opening a file, which is a hdf5 file but no mz5 file, a runtime_error is thrown.

Parameters:

filename	file name
op	open policy
configuration	configuration used to determine chunk and buffer sizes

pwiz::msdata::mz5::Connection_mz5::~Connection_mz5 ( )

Closes all open datasets and flushes file to filesystem.

Member Function Documentation

void pwiz::msdata::mz5::Connection_mz5::createAndWrite1DDataSet	(	hsize_t	size,
		void *	data,
		const Configuration_mz5::MZ5DataSets	v
	)

Creates and write a one dimensional dataset.

Parameters:

size	size of the dataset
data	void pointer to the dataset beginning
v	dataset enumeration value

void pwiz::msdata::mz5::Connection_mz5::extendData	(	const std::vector< double > &	d1,
		const Configuration_mz5::MZ5DataSets	v
	)

Extends data of to a dataset.

This method automatically uses an internal buffer to write the data and calls extendsAndWrite1DDataSet()

Parameters:

d1	data
v	dataset enumeration value

const std::map<Configuration_mz5::MZ5DataSets, size_t>& pwiz::msdata::mz5::Connection_mz5::getFields ( )

Returns a list of all existing datasets in this file.

void* pwiz::msdata::mz5::Connection_mz5::readDataSet	(	Configuration_mz5::MZ5DataSets	v,
		size_t &	dsend,
		void *	ptr = `0`
	)

Reads a dataset.

If no pointer is set, this method will allocate the needed mememory with calloc. To regain the memory call clean().

Parameters:

v	dataset enumeration value
dsend	dataset size
ptr	start pointer where the data should be written to.

Returns:: pointer to the data

void pwiz::msdata::mz5::Connection_mz5::clean	(	const Configuration_mz5::MZ5DataSets	v,
		void *	data,
		const size_t	dsend
	)

Clean up of open datasets and destruction of corresponding data elements.

This method calls vlenReclaim, free and close.

Parameters:

v	dataset enumeration value
data	pointer to the beginning of the data
dsend	length of the data.

void pwiz::msdata::mz5::Connection_mz5::getData	(	std::vector< double > &	data,
		const Configuration_mz5::MZ5DataSets	v,
		const hsize_t	start,
		const hsize_t	end
	)

Gets data from a numerical dataset and writes it to the vector.

This method is used to get mz,intensity and time.

Parameters:

data	data vector
v	dataset enumeration value
start	start index
end	end index

const Configuration_mz5& pwiz::msdata::mz5::Connection_mz5::getConfiguration ( )

Getter.

Returns:: current configuration

H5::DSetCreatPropList pwiz::msdata::mz5::Connection_mz5::getCParm	(	int	rank,
		const Configuration_mz5::MZ5DataSets &	v,
		const hsize_t &	datadim
	)

private

Creates a DSetCreatPropList for a dataset.

Parameters:

rank	dimensionality of dataset
dataset	dataset used to determine the name
datadim	data dimensions

Returns:: DSetCreatPropList

H5::DataSet pwiz::msdata::mz5::Connection_mz5::getDataSet	(	int	rank,
		hsize_t *	dim,
		hsize_t *	maxdim,
		const Configuration_mz5::MZ5DataSets	v
	)

private

Creates a dataset.

Parameters:

rank	dimensionality of the dataset
dim	size of each dimension
maxdim	maximal size of each dimension
v	dataset enumeration value

Returns:: dataset

void pwiz::msdata::mz5::Connection_mz5::readFile ( )

private

Initializes a file and read internal mz5 information.

Will throw a runtime_error when the file is not a mz5 file.

void pwiz::msdata::mz5::Connection_mz5::extendAndWrite1DDataSet	(	const H5::DataSet &	dataset,
		const std::vector< double > &	d1
	)

private

Extends and appends data to an existing dataset with no buffer.

Parameters:

dataset	dataset
d1	data

void pwiz::msdata::mz5::Connection_mz5::addToBuffer	(	std::vector< double > &	b,
		const std::vector< double > &	d1,
		const size_t	bs,
		const H5::DataSet &	dataset
	)

private

Internal method to add data to a buffer.

Parameters:

b	buffer
d1	data
bs	buffer size
dataset	dataset

void pwiz::msdata::mz5::Connection_mz5::flush ( const Configuration_mz5::MZ5DataSets v )

private

Flushes all data to the hard drive.

Parameters:

v	dataset enumeration value

void pwiz::msdata::mz5::Connection_mz5::close ( )

private

Closes the file and flushes all open buffers/datasets.

Member Data Documentation

std::map<Configuration_mz5::MZ5DataSets, size_t> pwiz::msdata::mz5::Connection_mz5::fields_

private

Existing field in file.

Definition at line 207 of file Connection_mz5.hpp.

H5::H5File* pwiz::msdata::mz5::Connection_mz5::file_

private

MZ5 file reference.

Definition at line 211 of file Connection_mz5.hpp.

Configuration_mz5 pwiz::msdata::mz5::Connection_mz5::config_

mutableprivate

mz5 configuration object.

Definition at line 215 of file Connection_mz5.hpp.

std::map<Configuration_mz5::MZ5DataSets, H5::DataSet> pwiz::msdata::mz5::Connection_mz5::bufferMap_

private

Mapping from a dataset enumeration value to the dataset.

Definition at line 219 of file Connection_mz5.hpp.

std::map<Configuration_mz5::MZ5DataSets, std::vector<double> > pwiz::msdata::mz5::Connection_mz5::buffers_

private

Mapping from a dataset enumeration value to a buffer.

Definition at line 223 of file Connection_mz5.hpp.

bool pwiz::msdata::mz5::Connection_mz5::closed_

private

Flag whether file is closed or not.

Definition at line 227 of file Connection_mz5.hpp.

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

/Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/msdata/mz5/Connection_mz5.hpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation