ms_crosslinking_settings Class Reference [Mascot configuration files module]

Settings element in crosslinking.xml More...

#include <ms_crosslinking_settings.hpp>

Inheritance diagram for ms_crosslinking_settings:

Collaboration diagram for ms_crosslinking_settings:

List of all members.

Public Member Functions
	ms_crosslinking_settings ()
	Default constructor.
	ms_crosslinking_settings (const ms_crosslinking_settings &src)
	Copying constructor.
virtual	~ms_crosslinking_settings ()
	Destructor.
void	appendParameter (const ms_crosslinking_parameter *item)
	Adds a new parameter at the end of the list.
virtual void	clearParameters ()
	Deletes all parameters from the list.
void	copyFrom (const ms_crosslinking_parameters *right)
	Copies all content from another instance.
void	copyFrom (const ms_crosslinking_settings *right)
	Copies all content from another instance.
void	defaultValues ()
	Call this member if you want to start again.
virtual bool	deleteParameterByName (const char *name)
	Remove a parameter from the list in memory by its unique name.
virtual bool	deleteParameterByNumber (const int idx)
	Remove a parameter from the list in memory by its index.
virtual int	getNumberOfParameters () const
	Returns the number of parameters held.
const ms_crosslinking_parameter *	getParameterByName (const char *name) const
	Returns a parameter object by its name or a null value in case of not found.
const ms_crosslinking_parameter *	getParameterByNumber (const int idx) const
	Returns a parameter object by its number.
virtual std::string	getParameterSchemaType () const
	Obtain a symbolic name for the parameter element schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
ms_crosslinking_settings &	operator= (const ms_crosslinking_settings &right)
	C++ style assignment operator.
bool	updateParameterByName (const char *name, const ms_crosslinking_parameter *param)
	Update the information for a specific parameter refering to it by its unique name.
bool	updateParameterByNumber (const int idx, const ms_crosslinking_parameter *param)
	Update the information for a specific parameter refering to it by its index.
std::string	validateDeep (const ms_xml_schema *pSchemaFileObj) const
	Performs validation of all child elements in addition to 'shallow' validation.
std::string	validateShallow (const ms_xml_schema *pSchemaFileObj) const
	Performs simple validation of the top-level elements only.

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Detailed Description

Settings element in crosslinking.xml

The settings section contains a list of parameters. These define the "business logic" for the crosslinking strategy.

These settings are intended for upstream (downstream) processing before (after) the spectrum has been matched:

• AssumeLinear: fragments with this charge or less are assumed not to include linked peptide (absolute value)
• AssumeLinked: fragments with this charge or more are assumed to include linked peptide (absolute value)
• SignatureScan: identifier(s) for scans to be inspected for signature peaks (see below)
• SignatureType: one of "reporter", "doublet", "triplet", "quadruplet"
• SignatureComp: depends on SignatureType, and specified as an elemental composition. The signature could be a single delta, multiple deltas or one or more reporter peaks.
• SignatureSN: minimum S/N for signature peak(s)
• SignatureStringency: one of "low", "medium", "high"
• SignatureTop: number of the most intense peaks that are candidates to be signature peaks
• MatchPair: identifier(s) for scans that may include fragments from both peptides in a pair (see below)
• MatchSingle: identifier(s) for scans that may include fragments from one peptide only (see below)

Scan identifier format for SignatureScan, MatchPair and MatchSingle is a comma-separated list of tokens from:

• CID
• ETD
• MS1
• MS2
• MS3

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Constructor & Destructor Documentation

ms_crosslinking_settings

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_crosslinking_settings

(

const ms_crosslinking_settings &

src )

Copying constructor.

Parameters:

src	another instance of this class to copy the content from.

---

Member Function Documentation

void copyFrom

(

const ms_crosslinking_settings *

right )

Copies all content from another instance.

Parameters:

right

another instance of this class to copy the content from.

void copyFrom

(

const ms_crosslinking_parameters *

right )

[inherited]

Copies all content from another instance.

Parameters:

right

another instance of this class to copy the content from.

bool deleteParameterByName

(

const char *

name )

[virtual, inherited]

Remove a parameter from the list in memory by its unique name.

Parameters:

name	name of the parameter for deletion.

Returns:

TRUE if the parameter has been found and successfully deleted and FALSE otherwise.

Implements ms_xml_parameters.

bool deleteParameterByNumber

(

const int

idx )

[virtual, inherited]

Remove a parameter from the list in memory by its index.

Parameters:

idx	number of the parameter for deletion from 0 to (getNumberOfParameters() - 1).

Returns:

TRUE if the parameter has been found and successfully deleted and FALSE otherwise.

Implements ms_xml_parameters.

int getNumberOfParameters

(

)

const [virtual, inherited]

Returns the number of parameters held.

Returns:

total number of parameters in the list.

Implements ms_xml_parameters.

const ms_crosslinking_parameter * getParameterByName

(

const char *

name )

const [inherited]

Returns a parameter object by its name or a null value in case of not found.

Parameters:

name	name of the parameter to find.

Returns:

a read-only pointer to a parameter object. See Maintaining object references: two rules of thumb.

const ms_crosslinking_parameter * getParameterByNumber

(

const int

idx )

const [inherited]

Returns a parameter object by its number.

Parameters:

idx	number of the parameter from 0 to (getNumberOfParameters() - 1).

Returns:

a read-only pointer to a parameter object. See Maintaining object references: two rules of thumb.

std::string getParameterSchemaType

(

)

const [virtual]

Obtain a symbolic name for the parameter element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns:

symbolic type name for the element.

Reimplemented from ms_crosslinking_parameters.

std::string getSchemaType

(

)

const [virtual]

Returns name of the schema type that can be used to validate this element.

Additional information about the current object can be retrieved from the associated XML schema file. Every element in an XML document is defined with a named type, which you can use to find out what kind of limits (numerical or otherwise) are defined for values of that type.

See also:

validateShallow(), validateDeep()

Returns:

a symbolic fully qualified type name (for example, "mxm:nameType").

Reimplemented from ms_crosslinking_parameters.

ms_crosslinking_settings & operator=

(

const ms_crosslinking_settings &

right )

C++ style assignment operator.

Parameters:

right

another instance of this class to copy the content from.

Returns:

reference to the current object

bool updateParameterByName	(	const char *	name,
		const ms_crosslinking_parameter *	param
	)		[inherited]

Update the information for a specific parameter refering to it by its unique name.

Parameters:

name	name of the parameter for updating.
param	an object to copy the content from.

Returns:

TRUE if the parameter has been found and successfully updated and FALSE otherwise.

bool updateParameterByNumber	(	const int	idx,
		const ms_crosslinking_parameter *	param
	)		[inherited]

Update the information for a specific parameter refering to it by its index.

Parameters:

idx	number of the parameter for updating from 0 to (getNumberOfParameters() - 1).
param	an object to copy the content from.

Returns:

TRUE if the parameter has been found and successfully updated and FALSE otherwise.

std::string validateDeep

(

const ms_xml_schema *

pSchemaFileObj )

const [inherited]

Performs validation of all child elements in addition to 'shallow' validation.

The current object can be checked against an XML schema. When using this method all possible checks are performed. However, this is not a substitute for the schema: some schema-defined constraint are not applied (unique fields, foreign keys etc.).

In order to make sure that current object is free from all syntax errors validate it as a part of the whole document.

See also:

validateShallow(), getSchemaType()

Parameters:

pSchemaFileObj

a valid schema object instance to validate against.

Returns:

user-friendly description of any errors found during validation or an empty string if no errors detected.

Reimplemented in ms_quant_average, ms_quant_integration, ms_quant_multiplex, ms_quant_normalisation, ms_quant_outliers, ms_quant_precursor, ms_quant_quality, ms_quant_replicate, and ms_quant_reporter.

std::string validateShallow

(

const ms_xml_schema *

pSchemaFileObj )

const [inherited]

Performs simple validation of the top-level elements only.

The current object can be checked against some basic constraints in a schema without looking at children element types. When using this method only the current object and children derived from standard types (for example, restrictions with enumerations) are checked. For more thorough validation, use validateDeep().

See also:

getSchemaType()

Parameters:

pSchemaFileObj

a valid schema object instance to validate against.

Returns:

user-friendly description of any errors found during validation or an empty string if no errors detected.

Reimplemented in ms_quant_average, ms_quant_integration, ms_quant_multiplex, ms_quant_normalisation, ms_quant_outliers, ms_quant_precursor, ms_quant_quality, ms_quant_replicate, and ms_quant_reporter.

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

• ms_crosslinking_settings.hpp
• ms_crosslinking_settings.cpp