SourceFile Class Reference

Description of a file location, used to store the origin of (meta) data. More...

#include <OpenMS/METADATA/SourceFile.h>

Inheritance diagram for SourceFile:

Collaboration diagram for SourceFile:

Public Types
enum class	ChecksumType { UNKNOWN_CHECKSUM , SHA1 , MD5 , SIZE_OF_CHECKSUMTYPE }
	Type of the checksum. More...
Public Types inherited from MetaInfoInterface
using	MetaInfoConstIterator = MetaInfo::const_iterator
	Const iterator type for iterating over meta info entries.

Public Member Functions
	SourceFile ()
	Constructor.
	SourceFile (const SourceFile &)=default
	Copy constructor.
	SourceFile (SourceFile &&)=default
	Move constructor.
	~SourceFile () override
	Destructor.
SourceFile &	operator= (const SourceFile &)=default
	Assignment operator.
SourceFile &	operator= (SourceFile &&)=default
	Move assignment operator.
bool	operator== (const SourceFile &rhs) const
	Equality operator.
bool	operator!= (const SourceFile &rhs) const
	Equality operator.
const std::string &	getNameOfFile () const
	returns the file name
void	setNameOfFile (const std::string &name_of_file)
	sets the file name
const std::string &	getPathToFile () const
	returns the file path
void	setPathToFile (const std::string &path_path_to_file)
	sets the file path
float	getFileSize () const
	returns the file size in MB
void	setFileSize (float file_size)
	sets the file size in MB
const std::string &	getFileType () const
	returns the file type
void	setFileType (const std::string &file_type)
	sets the file type
const std::string &	getChecksum () const
	returns the file's checksum
void	setChecksum (const std::string &checksum, ChecksumType type)
	sets the file's checksum
ChecksumType	getChecksumType () const
	returns the checksum type
const std::string &	getNativeIDType () const
	Returns the native ID type of the spectra.
void	setNativeIDType (const std::string &type)
	Sets the native ID type of the spectra.
const std::string &	getNativeIDTypeAccession () const
	Returns the nativeID of the spectra.
void	setNativeIDTypeAccession (const std::string &accesssion)
	Sets the native ID of the spectra.
Public Member Functions inherited from CVTermList
	CVTermList ()=default
	Defaults constructor.
	CVTermList (const CVTermList &)=default
	Copy constructor.
	CVTermList (CVTermList &&) noexcept
	Move constructor.
virtual	~CVTermList ()
	Destructor.
CVTermList &	operator= (const CVTermList &rhs) &=default
	Assignment operator.
CVTermList &	operator= (CVTermList &&) &=default
	Move assignment operator.
void	setCVTerms (const std::vector< CVTerm > &terms)
	sets the CV terms
void	replaceCVTerm (const CVTerm &cv_term)
	replaces the specified CV term
void	replaceCVTerms (const std::vector< CVTerm > &cv_terms, const std::string &accession)
	replaces the specified CV terms using the given accession number
void	replaceCVTerms (const std::map< std::string, std::vector< CVTerm > > &cv_term_map)
	replaces all cv terms with a map (can be obtained via getCVTerms)
void	consumeCVTerms (const std::map< std::string, std::vector< CVTerm > > &cv_term_map)
	merges the given map into the member map, no duplicate checking
const std::map< std::string, std::vector< CVTerm > > &	getCVTerms () const
	returns the accession string of the term
void	addCVTerm (const CVTerm &term)
	adds a CV term
bool	operator== (const CVTermList &cv_term_list) const
	equality operator
bool	operator!= (const CVTermList &cv_term_list) const
	inequality operator
bool	hasCVTerm (const std::string &accession) const
	checks whether the term has a value
bool	empty () const
	return true if no terms are available
Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()=default
	Constructor.
	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor.
	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor.
	~MetaInfoInterface ()
	Destructor.
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator.
MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator.
void	swap (MetaInfoInterface &rhs)
	Swap contents.
bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator.
bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator.
const DataValue &	getMetaValue (const std::string &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found.
DataValue	getMetaValue (const std::string &name, const DataValue &default_value) const
	Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found.
DataValue	getMetaValue (UInt index, const DataValue &default_value) const
	Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found
bool	metaValueExists (const std::string &name) const
	Returns whether an entry with the given name exists.
bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists.
void	setMetaValue (const std::string &name, const DataValue &value)
	Sets the DataValue corresponding to a name.
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index.
void	removeMetaValue (const std::string &name)
	Removes the DataValue corresponding to name if it exists.
void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to index if it exists.
void	addMetaValues (const MetaInfoInterface &from)
void	getKeys (std::vector< std::string > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
bool	isMetaEmpty () const
	Returns if the MetaInfo is empty.
void	clearMetaInfo ()
	Removes all meta values.
MetaInfoConstIterator	metaBegin () const
	Returns a const iterator to the beginning of the meta info entries.
MetaInfoConstIterator	metaEnd () const
	Returns a const iterator to the end of the meta info entries.
Size	metaSize () const
	Returns the number of meta info entries.

Static Public Member Functions
static StringList	getAllNamesOfChecksumType ()
	returns all checksum type names known to OpenMS
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry.

Static Public Attributes
static const std::string	NamesOfChecksumType [static_cast< size_t >(ChecksumType::SIZE_OF_CHECKSUMTYPE)]
	Names of checksum types.

Protected Attributes
std::string	name_of_file_
std::string	path_to_file_
double	file_size_
std::string	file_type_
std::string	checksum_
ChecksumType	checksum_type_ = SourceFile::ChecksumType::UNKNOWN_CHECKSUM
std::string	native_id_type_
std::string	native_id_type_accession_
Protected Attributes inherited from CVTermList
std::map< std::string, std::vector< CVTerm > >	cv_terms_
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_ = nullptr
	Pointer to the MetaInfo object.

Additional Inherited Members
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist.

Detailed Description

Description of a file location, used to store the origin of (meta) data.

Member Enumeration Documentation

ChecksumType

enum class ChecksumType

strong

Type of the checksum.

Enumerator
UNKNOWN_CHECKSUM	Unknown checksum type.
SHA1	Secure Hash Algorithm-1.
MD5	Message-Digest algorithm 5.
SIZE_OF_CHECKSUMTYPE

Constructor & Destructor Documentation

SourceFile() [1/3]

SourceFile

(

)

Constructor.

SourceFile() [2/3]

SourceFile ( const SourceFile &  )

default

Copy constructor.

SourceFile() [3/3]

SourceFile ( SourceFile &&  )

default

Move constructor.

~SourceFile()

~SourceFile ( )

override

Destructor.

Member Function Documentation

getAllNamesOfChecksumType()

static StringList getAllNamesOfChecksumType ( )

static

returns all checksum type names known to OpenMS

getChecksum()

const std::string & getChecksum

(

)

const

returns the file's checksum

getChecksumType()

ChecksumType getChecksumType

(

)

const

returns the checksum type

getFileSize()

float getFileSize

(

)

const

returns the file size in MB

getFileType()

const std::string & getFileType

(

)

const

returns the file type

getNameOfFile()

const std::string & getNameOfFile

(

)

const

returns the file name

getNativeIDType()

const std::string & getNativeIDType

(

)

const

Returns the native ID type of the spectra.

getNativeIDTypeAccession()

const std::string & getNativeIDTypeAccession

(

)

const

Returns the nativeID of the spectra.

getPathToFile()

const std::string & getPathToFile

(

)

const

returns the file path

operator!=()

bool operator!=

(

const SourceFile &

rhs

)

const

Equality operator.

operator=() [1/2]

SourceFile & operator= ( const SourceFile &  )

default

Assignment operator.

operator=() [2/2]

SourceFile & operator= ( SourceFile &&  )

default

Move assignment operator.

operator==()

bool operator==

(

const SourceFile &

rhs

)

const

Equality operator.

setChecksum()

void setChecksum	(	const std::string &	checksum,
		ChecksumType	type
	)

sets the file's checksum

setFileSize()

void setFileSize

(

float

file_size

)

sets the file size in MB

Referenced by XMassFile::load().

setFileType()

void setFileType

(

const std::string &

file_type

)

sets the file type

Referenced by XMassFile::load().

setNameOfFile()

void setNameOfFile

(

const std::string &

name_of_file

)

sets the file name

Referenced by XMassFile::load().

setNativeIDType()

void setNativeIDType

(

const std::string &

type

)

Sets the native ID type of the spectra.

setNativeIDTypeAccession()

void setNativeIDTypeAccession

(

const std::string &

accesssion

)

Sets the native ID of the spectra.

setPathToFile()

void setPathToFile

(

const std::string &

path_path_to_file

)

sets the file path

Referenced by XMassFile::load().

Member Data Documentation

checksum_

std::string checksum_

protected

checksum_type_

ChecksumType checksum_type_ = SourceFile::ChecksumType::UNKNOWN_CHECKSUM

protected

file_size_

double file_size_

protected

file_type_

std::string file_type_

protected

name_of_file_

std::string name_of_file_

protected

NamesOfChecksumType

const std::string NamesOfChecksumType[static_cast< size_t >(ChecksumType::SIZE_OF_CHECKSUMTYPE)]

static

Names of checksum types.

native_id_type_

std::string native_id_type_

protected

native_id_type_accession_

std::string native_id_type_accession_

protected

path_to_file_

std::string path_to_file_

protected