ms_libraryoptions Class Reference [Mascot configuration files module]

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

#include <ms_libraryoptions.hpp>

Inheritance diagram for ms_libraryoptions:

Collaboration diagram for ms_libraryoptions:

List of all members.

Public Member Functions
	ms_libraryoptions ()
	Default constructor.
	ms_libraryoptions (const ms_libraryoptions &src)
	Copying constructor.
	~ms_libraryoptions ()
	Destructor.
void	copyFrom (const ms_libraryoptions *right)
	Can be used to copy content from another instance.
void	defaultValues ()
	Initializes the instance.
void	dropSpectralLibrary (const char *spectralLibraryName)
	Remove all references to the specified spectral library.
std::string	getLibraryName (const int num) const
	Return the name of the library.
int	getNumberOfLibraries () const
	Return the number of libraries.
std::string	getPreceedingComments () const
	Returns any comments preceeding the section.
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	setPreceedingComments (const std::string &comments)
	Sets any comments preceeding the section.
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.

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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.

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Constructor & Destructor Documentation

ms_libraryoptions

(

)

Default constructor.

Create an object with no options

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

(

)

Destructor.

Frees any memory

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Member Function Documentation

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

void defaultValues

(

)

Initializes the instance.

Remove details for all the libraries

Reimplemented from ms_customproperty.

void dropSpectralLibrary

(

const char *

spectralLibraryName )

Remove all references to the specified spectral library.

Parameters:

spectralLibraryName

is the (short) name of the library

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()

int getNumberOfLibraries

(

)

const

Return the number of libraries.

Returns:

The number of libraries with parameters in the section

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

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

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.

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.

See also, getToleranceInPPM(), setToleranceInPPM() and setToleranceInDa()

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

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.

See also, setToleranceInPPM(), getToleranceInDa() and setToleranceInDa()

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

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

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'

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

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.

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

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.

See also, getToleranceInPPM(), setToleranceInPPM() and getToleranceInDa()

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

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.

See also, getToleranceInPPM(), getToleranceInDa() and setToleranceInDa()

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

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

• ms_libraryoptions.hpp
• ms_libraryoptions.cpp