ms_quant_normalisation Class Reference

An object of this class represent a single normalisation element in quantitation.xml. More...

#include <ms_quant_normalisation.hpp>

Inheritance diagram for ms_quant_normalisation:

Collaboration diagram for ms_quant_normalisation:

Public Member Functions
	ms_quant_normalisation ()
	Default constructor.
	ms_quant_normalisation (const ms_quant_normalisation &src)
	Copying constructor.
virtual	~ms_quant_normalisation ()
	Destructor.
void	appendParameter (const ms_quant_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_quant_normalisation *right)
	Copies all content from another instance.
void	copyFrom (const ms_quant_parameters *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.
void	dropMethod ()
	Delete the method attribute.
void	dropPeptides ()
	Delete the peptides element.
void	dropProteins ()
	Delete the proteins element.
std::string	getMethod () const
	Returns the value of the method attribute.
std::string	getMethodSchemaType () const
	Obtain a symbolic name for the method attribute schema type.
virtual int	getNumberOfParameters () const
	Returns the number of parameters held.
const ms_quant_parameter *	getParameterByName (const char *name) const
	Returns a parameter object by its name or a null value in case of not found.
const ms_quant_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.
const ms_quant_normalisation_peptides *	getPeptides () const
	Returns a pointer to the peptides element.
std::string	getPeptidesSchemaType () const
	Obtain a symbolic name for the peptides element schema type.
const ms_quant_normalisation_proteins *	getProteins () const
	Returns a pointer to the proteins element.
std::string	getProteinsSchemaType () const
	Obtain a symbolic name for the proteins element schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
bool	haveMethod () const
	Indicates presence of the method attribute.
bool	havePeptides () const
	Indicates presence of the peptides element.
bool	haveProteins () const
	Indicates presence of the proteins element.
ms_quant_normalisation &	operator= (const ms_quant_normalisation &right)
	C++ style assignment operator.
void	setMethod (const char *value)
	Set a custom value for the method attribute.
void	setPeptides (const ms_quant_normalisation_peptides *peptides)
	Supply custom content for peptides element.
void	setProteins (const ms_quant_normalisation_proteins *proteins)
	Supply custom content for the proteins element.
bool	updateParameterByName (const char *name, const ms_quant_parameter *param)
	Update the information for a specific parameter refering to it by its unique name.
bool	updateParameterByNumber (const int idx, const ms_quant_parameter *param)
	Update the information for a specific parameter refering to it by its index.
virtual std::string	validateDeep (const ms_xml_schema *pSchemaFileObj) const
	Performs validation of all child elements in addition to 'shallow' validation.
virtual std::string	validateShallow (const ms_xml_schema *pSchemaFileObj) const
	Performs simple validation of the top-level elements only.

Detailed Description

An object of this class represent a single normalisation element in quantitation.xml.

Method of normalising ratios for a complete data set.

Constructor & Destructor Documentation

ms_quant_normalisation() [1/2]

ms_quant_normalisation

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_normalisation() [2/2]

ms_quant_normalisation

(

const ms_quant_normalisation &

src

)

Copying constructor.

Parameters

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

Member Function Documentation

appendParameter()

void appendParameter ( const ms_quant_parameter *  item )

inherited

Adds a new parameter at the end of the list.

Parameters

item	an instance of parameter object to copy content from.

copyFrom() [1/2]

void copyFrom

(

const ms_quant_normalisation *

right

)

Copies all content from another instance.

Parameters

right

another instance of this class to copy the content from.

copyFrom() [2/2]

void copyFrom ( const ms_quant_parameters *  right )

inherited

Copies all content from another instance.

Parameters

right

another instance of this class to copy the content from.

defaultValues()

void defaultValues

(

)

Call this member if you want to start again.

All internal values are reset to their defaults, as if the object had been freshly created with the default constructor.

deleteParameterByName()

bool deleteParameterByName ( const char *  name )

virtualinherited

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.

deleteParameterByNumber()

bool deleteParameterByNumber ( const int  idx )

virtualinherited

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.

dropMethod()

void dropMethod

(

)

Delete the method attribute.

Disables the attribute until it is re-set.

dropPeptides()

void dropPeptides

(

)

Delete the peptides element.

Deletes the element until it is re-set.

dropProteins()

void dropProteins

(

)

Delete the proteins element.

Deletes the element until it is re-set.

getMethod()

std::string getMethod

(

)

const

Returns the value of the method attribute.

• Average: For each ratio, the geometric mean of all reported values for peptide matches is made unity.
• Median: For each ratio, the median of all reported values for peptide matches is made unity.
• Sum: (Reporter protocol only) The total intensity of each reporter ion, summed across all MS/MS spectra, is made equal.

Sum is only available for reporter protocol; average and median are only available when all protein hits are processed (i.e. REPORT=AUTO).

Returns

current value of the method attribute.

getMethodSchemaType()

std::string getMethodSchemaType

(

)

const

Obtain a symbolic name for the method attribute 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.

getNumberOfParameters()

int getNumberOfParameters ( ) const

virtualinherited

Returns the number of parameters held.

Returns

total number of parameters in the list.

Implements ms_xml_parameters.

getParameterByName()

const ms_quant_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.

getParameterByNumber()

const ms_quant_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.

getParameterSchemaType()

std::string getParameterSchemaType ( ) const

virtualinherited

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.

Implements ms_xml_parameters.

getPeptides()

const ms_quant_normalisation_peptides * getPeptides

(

)

const

Returns a pointer to the peptides element.

List of peptide sequences to be used for normalisation.

Returns

a read-only pointer to an object with the current element content. See Maintaining object references: two rules of thumb.

getPeptidesSchemaType()

std::string getPeptidesSchemaType

(

)

const

Obtain a symbolic name for the peptides 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.

getProteins()

const ms_quant_normalisation_proteins * getProteins

(

)

const

Returns a pointer to the proteins element.

List of protein accessions to be used for normalisation.

Returns

a read-only pointer to an object with the current element content. See Maintaining object references: two rules of thumb.

getProteinsSchemaType()

std::string getProteinsSchemaType

(

)

const

Obtain a symbolic name for the proteins 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.

getSchemaType()

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, "mqm:nameType").

Reimplemented from ms_quant_parameters.

haveMethod()

bool haveMethod

(

)

const

Indicates presence of the method attribute.

You should always check for the presence of an attribute before retrieving its actual value.

Returns

TRUE if the attribute is present in current element and FALSE otherwise.

havePeptides()

bool havePeptides

(

)

const

Indicates presence of the peptides element.

Returns

TRUE if the element is present and FALSE otherwise.

haveProteins()

bool haveProteins

(

)

const

Indicates presence of the proteins element.

Returns

TRUE if the element is present and FALSE otherwise.

operator=()

ms_quant_normalisation & operator=

(

const ms_quant_normalisation &

right

)

C++ style assignment operator.

Parameters

right

another instance of this class to copy the content from.

Returns

reference to the current object

setMethod()

void setMethod

(

const char *

value

)

Set a custom value for the method attribute.

An attribute becomes present after it is value has been set at least once. To disable it again call dropMethod().

Parameters

value

a new value for the attribute.

setPeptides()

void setPeptides

(

const ms_quant_normalisation_peptides *

peptides

)

Supply custom content for peptides element.

Parameters

peptides

a new content for the element.

setProteins()

void setProteins

(

const ms_quant_normalisation_proteins *

proteins

)

Supply custom content for the proteins element.

Parameters

proteins

a new content for the element.

updateParameterByName()

bool updateParameterByName ( const char *  name, const ms_quant_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.

updateParameterByNumber()

bool updateParameterByNumber ( const int  idx, const ms_quant_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.

validateDeep()

std::string validateDeep ( const ms_xml_schema *  pSchemaFileObj ) const

virtual

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.

validateShallow()

std::string validateShallow ( const ms_xml_schema *  pSchemaFileObj ) const

virtual

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.

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

• ms_quant_normalisation.hpp
• ms_quant_normalisation.cpp