Represents the LibraryOptions section of mascot.dat. More...

#include <ms_libraryoptions.hpp>

Inheritance diagram for ms_libraryoptions:

Collaboration diagram for ms_libraryoptions:

Public Member Functions
	ms_libraryoptions ()
	Default constructor.

	ms_libraryoptions (const ms_libraryoptions &src)
	Copying constructor.

	~ms_libraryoptions ()
	Destructor.

void	appendProperty (const char name, const char value, const char *delimiter, const bool bFirstPlace=false)
	Adds a new property with the given parameters.

void	appendText (const char *line, const bool bFirstPlace=false)
	Adds a new non-parsed property.

void	copyFrom (const ms_customproperty *src)
	Copies all properties and comments from another instance.

void	copyFrom (const ms_libraryoptions *right)
	Can be used to copy content from another instance.

void	defaultValues ()
	Initializes the instance.

void	delNonEmpty ()
	Deletes all non-comment properties.

void	delProp (const char *name)
	Deletes all properties with the specified name.

void	delPropByNumber (const int index)
	Deletes a single property with the specified number only.

void	delPropStart (const char *nameBeginning)
	Deletes all properties whose names start with the given string.

void	dropSpectralLibrary (const char *spectralLibraryName)
	Remove all references to the specified spectral library.

int	findProperty (const char *name, const int startFrom=0) const
	Searches the list for a property with the given name.

int	findPropertyBeginning (const char *nameBeginning, const int startFrom=0) const
	Searches the list for a property with the partially matching name.

std::string	getDefaultDelimiter () const
	Return current default delimiter string used for parsing/storing properties.

std::string	getDelimiterByNumber (const int index) const
	Returns a specific delimiter used for the property.

std::string	getLibraryName (const int num) const
	Return the name of the library.

int	getNumberOfLibraries () const
	Return the number of libraries.

int	getNumberOfProperties () const
	Returns a total number of property/comment entries.

std::string	getPreceedingComments () const
	Returns any comments preceeding the section.

std::string	getPropertyName (const int index) const
	Returns a property name for a given index.

std::string	getPropValStringByName (const char *name) const
	Retrieves property value by name.

std::string	getPropValStringByNumber (const int index) const
	Retrieves property raw text values by number.

std::string	getReferenceFasta (const char *spectralLibraryName) const
	Returns the name of the Fasta database used as a reference for accessions for the spectral library.

std::string	getReferenceFastaTaxonomyTitle (const char *spectralLibraryName) const
	Returns the title of the taxonomy to use for the reference database.

double	getToleranceInDa (const char *spectralLibraryName) const
	Returns the tolerance of the data in spectral library.

double	getToleranceInPPM (const char *spectralLibraryName) const
	Returns the tolerance of the data in spectral library.

bool	isSectionAvailable () const
	Check whether the section has been actually read from the file.

ms_libraryoptions &	operator= (const ms_libraryoptions &right)
	Assignment operator for C++ client applications.

void	setDefaultDelimiter (const char *delim)
	Allows to set a specific delimiter string to be used when no property-specific delimiter is supplied.

void	setPreceedingComments (const std::string &comments)
	Sets any comments preceeding the section.

void	setPropertyName (const int index, const char *name)
	Changes name of the property with the given index.

void	setPropValBoolByName (const char *name, const bool value, const bool bFirstPlace=false)
	Changes a boolean value of the first entry with the given name or creates a new property if it is not found.

void	setPropValCharByName (const char *name, const char value, const bool bFirstPlace=false)
	Changes a single character value of the first entry with the given name or creates a new property if it is not found.

void	setPropValFloatByName (const char *name, const double value, const bool bFirstPlace=false)
	Changes an floating point value of the first entry with the given name or creates a new property if it is not found.

void	setPropValInt64ByName (const char *name, const INT64 value, const bool bFirstPlace=false)
	Changes a long 64-bit integer value of the first entry with the given name or creates a new property if it is not found.

void	setPropValIntByName (const char *name, const int value, const bool bFirstPlace=false)
	Changes an integer value of the first entry with the given name or creates a new property if it is not found.

void	setPropValStringByName (const char name, const char value, const bool bFirstPlace=false)
	Changes a string value of the first entry with the given name or creates a new property if it is not found.

void	setPropValStringByNumber (const int index, const char *value)
	Changes an string value of an existing property with the given index.

void	setReferenceFasta (const char spectralLibraryName, const char fastaDatabaseName, const char *taxonomyTitle)
	Sets the name of the Fasta database used as a reference for accessions for the spectral library.

void	setSectionAvailable (const bool value)
	Changes availability of the section, i.e. whether it should be saved in a file.

void	setToleranceInDa (const char *spectralLibraryName, double tolerance)
	Sets the tolerance of the data in spectral library.

void	setToleranceInPPM (const char *spectralLibraryName, double tolerance)
	Sets the tolerance of the data in spectral library.

bool	uncommentProp (const int index, const char *delimeter=0)
	Uncomments a line in the configuration file.

Detailed Description

Represents the LibraryOptions section of mascot.dat.

See : ms_datfile::getLibraryOptions and ms_datfile::setLibraryOptions

Also get yourselves acquainted with the base class ms_customproperty. It facilitates the following tasks:

Retrieving an unsupported property.
Retrieving a raw/text/XML property representation.
Checking for existence of a certain property rather than dealing with its default value.
Accessing commented lines in a section.

More functionality is described in the documentation for ms_customproperty.

Constructor & Destructor Documentation

◆ ms_libraryoptions() [1/2]

ms_libraryoptions ( )

Default constructor.

Create an object with no options

◆ ms_libraryoptions() [2/2]

ms_libraryoptions ( const ms_libraryoptions & src )

Copying constructor.

C++ only. Use copyFrom from other languages.

Parameters

src	is the source options to copy into the new object

◆ ~ms_libraryoptions()

~ms_libraryoptions ( )

Destructor.

Frees any memory

Member Function Documentation

◆ appendProperty()

void appendProperty	(	const char *	name,
		const char *	value,
		const char *	delimiter,
		const bool	bFirstPlace = `false`
	)

inherited

Adds a new property with the given parameters.

Parameters

name	a property name to use.
value	a property value to use.
delimiter	a specific delimiter or an empty string for a default one to be used.
bFirstPlace	forces a new property to be put on top of the list.

◆ appendText()

void appendText	(	const char *	l,
		const bool	bFirstPlace = `false`
	)

inherited

Adds a new non-parsed property.

All property elements will be retrieved from the first parameter. Before calling this method, a specific default delimiter can be set using setDefaultDelimiter().

Parameters

l	raw text representation of the property to be parsed.
bFirstPlace	forces a new property to be put on top of the list.

◆ copyFrom()

void copyFrom ( const ms_libraryoptions * right )

Can be used to copy content from another instance.

Copy all the parameter for the libraries from right into the object

Parameters

right is the source library options

◆ defaultValues()

void defaultValues ( )

Initializes the instance.

Remove details for all the libraries

◆ delProp()

void delProp ( const char * str )

inherited

Deletes all properties with the specified name.

Parameters

str	Property name to find a match and then delete.

◆ delPropStart()

void delPropStart ( const char * str )

inherited

Deletes all properties whose names start with the given string.

Parameters

str	Beginning a first part of the property name to delete.

◆ dropSpectralLibrary()

void dropSpectralLibrary ( const char * spectralLibraryName )

Remove all references to the specified spectral library.

Parameters

spectralLibraryName is the (short) name of the library

◆ findProperty()

int findProperty	(	const char *	name,
		const int	startFrom = `0`
	)		const

inherited

Searches the list for a property with the given name.

If no property found with the given name -1 will be returned. There may be several property entries in the list with the same name.

Parameters

name	a property name to be found.
startFrom	a minimal property index to start search from.

Returns: a property index or -1 if no property found.

◆ findPropertyBeginning()

int findPropertyBeginning	(	const char *	nameBeginning,
		const int	startFrom = `0`
	)		const

inherited

Searches the list for a property with the partially matching name.

If no property found with the given name part -1 will be returned. There may be several property entries in the list whose names start with the given string.

Parameters

nameBeginning	first part of a property name to be found.
startFrom	a minimal property index to start search from.

Returns: a property index or -1 if no property found.

◆ getDefaultDelimiter()

std::string getDefaultDelimiter ( ) const

inherited

Return current default delimiter string used for parsing/storing properties.

Returns: default delimiter

◆ getDelimiterByNumber()

std::string getDelimiterByNumber ( const int index ) const

inherited

Returns a specific delimiter used for the property.

Parameters

index Index for which to get a delimiter

Returns: corresponding delimiter

◆ getLibraryName()

std::string getLibraryName ( const int num ) const

Return the name of the library.

Parameters

num	must be in the range 0 to getNumberOfLibraries() -1

Returns: the name of the library which can be used in other functions such as getReferenceFasta()

◆ getNumberOfLibraries()

int getNumberOfLibraries ( ) const

Return the number of libraries.

Returns: The number of libraries with parameters in the section

◆ getNumberOfProperties()

int getNumberOfProperties ( ) const

inherited

Returns a total number of property/comment entries.

Returns: Number of property/comment entries

◆ getPreceedingComments()

std::string getPreceedingComments ( ) const

inherited

Returns any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also: setPreceedingComments()

Returns: any comments preceeding the section

◆ getPropertyName()

std::string getPropertyName ( const int index ) const

inherited

Returns a property name for a given index.

Parameters

index property number from 0 to (getNumberOfProperties()-1).

Returns: Rroperty name of an empty string for comments.

◆ getPropValStringByName()

std::string getPropValStringByName ( const char * name ) const

inherited

Retrieves property value by name.

Don't use this method for comments as they all have empty name. Also note that there might be several entries corresponding to the same name . – only the first value will be returned. If in doubt use findProperty() and getPropValStringByNumber() instead.

Parameters

name	Name for which to get a property value

Returns: corresponding property value

◆ getPropValStringByNumber()

std::string getPropValStringByNumber ( const int index ) const

inherited

Retrieves property raw text values by number.

Parameters

index Index for which to get a property value

Returns: corresponding property value

◆ getReferenceFasta()

std::string getReferenceFasta ( const char * spectralLibraryName ) const

Returns the name of the Fasta database used as a reference for accessions for the spectral library.

A Spectral library is essentially a peptide library and will often not contain meaningful accessions. To get useful protein grouping in Mascot reports, it is recommended that users specify a 'reference' database. When a reference database is used, Mascot tries to find the peptide sequence from the library in the reference fasta, and if it is found then it adds the accession for that protein sequence to the search results.

See also: getReferenceFastaTaxonomyTitle()

Parameters

spectralLibraryName is the (short) name of the library

Returns: the (short) name of the reference fasta

◆ getReferenceFastaTaxonomyTitle()

std::string getReferenceFastaTaxonomyTitle ( const char * spectralLibraryName ) const

Returns the title of the taxonomy to use for the reference database.

The reference database may contain protein accessions from multiple taxa. If a suitable taxonomy index is configured, you can define the taxon to use for reference accessions. The returned value is the title string of an entry in the taxonomy configuration file (typically mascot/config/taxonomy).

See also: getReferenceFasta()

Parameters

spectralLibraryName is the (short) name of the library

Returns: the title of the taxon, or the empty string if not set.

◆ getToleranceInDa()

double getToleranceInDa ( const char * spectralLibraryName ) const

Returns the tolerance of the data in spectral library.

A spectral library is created using an instrument with a known tolerance and this tolerance is specified by the user when they enable the use of the library in Mascot. When the library is searched, the tolerance used is the square root of the sum of the squares of the data being searched and this value.

The tolerance of the library is specified in Da and ppm since the user may choose either units when they submit a search.

If spectralLibraryName does not exist, returns the default (0.6 Da)

Parameters

spectralLibraryName is the (short) name of the library

Returns: the tolerance of the data in the library

◆ getToleranceInPPM()

double getToleranceInPPM ( const char * spectralLibraryName ) const

Returns the tolerance of the data in spectral library.

A spectral library is created using an instrument with a known tolerance and this tolerance is specified by the user when they enable the use of the library in Mascot. When the library is searched, the tolerance used is the square root of the sum of the squares of the data being searched and this value.

The tolerance of the library is specified in Da and ppm since the user may choose either units when they submit a search.

If spectralLibraryName does not exist, returns the default (500ppm)

Parameters

spectralLibraryName is the (short) name of the library

Returns: the tolerance of the data in the library

◆ isSectionAvailable()

bool isSectionAvailable ( ) const

Check whether the section has been actually read from the file.

By default the LibraryOptions section is unavailable until it has been set to a different state.

The section does not have to exist in the mascot.dat file

Returns: true if the section exists

◆ operator=()

ms_libraryoptions & operator= ( const ms_libraryoptions & right )

Assignment operator for C++ client applications.

C++ only

Parameters

right is the source library options

Returns: a reference to 'this'

◆ setDefaultDelimiter()

void setDefaultDelimiter ( const char * delim )

inherited

Allows to set a specific delimiter string to be used when no property-specific delimiter is supplied.

Parameters

delim String to set the default delimiter

◆ setPreceedingComments()

void setPreceedingComments ( const std::string & comments )

inherited

Sets any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also: getPreceedingComments()

Parameters

comments any comments preceeding the section

◆ setPropertyName()

void setPropertyName	(	const int	index,
		const char *	name
	)

inherited

Changes name of the property with the given index.

Parameters

index	property number from 0 to (getNumberOfProperties()-1).
name	new name to be given to the property.

◆ setPropValBoolByName()

void setPropValBoolByName	(	const char *	name,
		const bool	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a boolean value of the first entry with the given name or creates a new property if it is not found.

A new value will be converted into 1 (for TRUE) or 0 (for FALSE) character.

Parameters

name	a name of the property to find or add.
value	a new boolean value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValCharByName()

void setPropValCharByName	(	const char *	name,
		const char	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a single character value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new single character value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValFloatByName()

void setPropValFloatByName	(	const char *	name,
		const double	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes an floating point value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new floating point value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValInt64ByName()

void setPropValInt64ByName	(	const char *	name,
		const INT64	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a long 64-bit integer value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new long 64-bit integer value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValIntByName()

void setPropValIntByName	(	const char *	name,
		const int	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes an integer value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new integer value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValStringByName()

void setPropValStringByName	(	const char *	name,
		const char *	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a string value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new string value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValStringByNumber()

void setPropValStringByNumber	(	const int	index,
		const char *	str
	)

inherited

Changes an string value of an existing property with the given index.

Parameters

index	an index of an existing property.
str	String value for the property.

◆ setReferenceFasta()

void setReferenceFasta	(	const char *	spectralLibraryName,
		const char *	fastaDatabaseName,
		const char *	taxonomyTitle
	)

Sets the name of the Fasta database used as a reference for accessions for the spectral library.

A Spectral library is essentially a peptide library and will often not contain meaningful accessions. To get useful protein grouping in Mascot reports, it is recommended that users specify a 'reference' database. When a reference database is used, Mascot tries to find the peptide sequence from the library in the reference fasta. If it is found, Mascot adds the accession for that protein sequence to the search results.

The reference database may contain protein accessions from multiple taxa. To restrict accesions to a particular taxon, give its title as the third argument. Titles typically come from the taxonomy configuration file (mascot/config/taxonomy). If left empty, there is no restriction.

Parameters

spectralLibraryName	is the (short) name of the library
fastaDatabaseName	is the (short) name of the reference database
taxonomyTitle	is the title of the taxon to use, or the empty string.

◆ setSectionAvailable()

void setSectionAvailable ( const bool value )

Changes availability of the section, i.e. whether it should be saved in a file.

The section does not have to exist in the mascot.dat file

Parameters

value set to true if the section exists

◆ setToleranceInDa()

void setToleranceInDa	(	const char *	spectralLibraryName,
		double	tolerance
	)

Sets the tolerance of the data in spectral library.

A spectral library is created using an instrument with a known tolerance and this tolerance is specified by the user when they enable the use of the library in Mascot. When the library is searched, the tolerance used is the square root of the sum of the squares of the data being searched and this value.

The tolerance of the library is specified in Da and ppm since the user may choose either units when they submit a search.

If spectralLibraryName does not exist, returns the default (500ppm)

Parameters

spectralLibraryName	is the (short) name of the library
tolerance	is the new tolerance for spectralLibraryName

◆ setToleranceInPPM()

void setToleranceInPPM	(	const char *	spectralLibraryName,
		double	tolerance
	)

Sets the tolerance of the data in spectral library.

A spectral library is created using an instrument with a known tolerance and this tolerance is specified by the user when they enable the use of the library in Mascot. When the library is searched, the tolerance used is the square root of the sum of the squares of the data being searched and this value.

The tolerance of the library is specified in Da and ppm since the user may choose either units when they submit a search.

If spectralLibraryName does not exist, this adds a new entry for the library and sets a default value for other parameters for the library

Parameters

spectralLibraryName	is the (short) name of the library
tolerance	is the new tolerance for spectralLibraryName

◆ uncommentProp()

bool uncommentProp	(	const int	index,
		const char *	delimeter = `0`
	)

inherited

Uncomments a line in the configuration file.

Removes a # and any white space. Finds the delimeter and extracts the property name and value.

Parameters

index	must be a value between 0 and getNumberOfProperties().
delimeter	will often be a space. If not supplied, the default delimeter will be used.

Returns: true if the delimiter was found, false otherwise

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

ms_libraryoptions.hpp
ms_libraryoptions.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ms_libraryoptions() [1/2]

◆ ms_libraryoptions() [2/2]

◆ ~ms_libraryoptions()

Member Function Documentation

◆ appendProperty()

◆ appendText()

◆ copyFrom()

◆ defaultValues()

◆ delProp()

◆ delPropStart()

◆ dropSpectralLibrary()

◆ findProperty()

◆ findPropertyBeginning()

◆ getDefaultDelimiter()

◆ getDelimiterByNumber()

◆ getLibraryName()

◆ getNumberOfLibraries()

◆ getNumberOfProperties()

◆ getPreceedingComments()

◆ getPropertyName()

◆ getPropValStringByName()

◆ getPropValStringByNumber()

◆ getReferenceFasta()

◆ getReferenceFastaTaxonomyTitle()

◆ getToleranceInDa()

◆ getToleranceInPPM()

◆ isSectionAvailable()

◆ operator=()

◆ setDefaultDelimiter()

◆ setPreceedingComments()

◆ setPropertyName()

◆ setPropValBoolByName()

◆ setPropValCharByName()

◆ setPropValFloatByName()

◆ setPropValInt64ByName()

◆ setPropValIntByName()

◆ setPropValStringByName()

◆ setPropValStringByNumber()

◆ setReferenceFasta()

◆ setSectionAvailable()

◆ setToleranceInDa()

◆ setToleranceInPPM()

◆ uncommentProp()