ms_quant_average Class Reference

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

#include <ms_quant_average.hpp>

Inheritance diagram for ms_quant_average:

Collaboration diagram for ms_quant_average:

Public Member Functions
	ms_quant_average ()
	Default constructor.
	ms_quant_average (const ms_quant_average &src)
	Copying constructor.
virtual	~ms_quant_average ()
	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_average *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	dropNumPeptides ()
	Delete the num_peptides attribute.
void	dropReferenceAccession ()
	Delete the reference_accession attribute.
void	dropReferenceAmount ()
	Delete the reference_amount attribute.
void	dropReferenceDatabase ()
	Delete the reference_database attribute.
void	dropSelection ()
	Delete the selection attribute.
virtual int	getNumberOfParameters () const
	Returns the number of parameters held.
int	getNumPeptides () const
	Returns the value of the num_peptides attribute.
std::string	getNumPeptidesSchemaType () const
	Obtain a symbolic name for the num_peptides attribute schema type.
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.
std::string	getReferenceAccession () const
	Returns the value of the reference_accession attribute.
std::string	getReferenceAccessionSchemaType () const
	Obtain a symbolic name for the reference_accession attribute schema type.
std::string	getReferenceAmount () const
	Returns the value of the reference_amount attribute.
std::string	getReferenceAmountSchemaType () const
	Obtain a symbolic name for the reference_amount attribute schema type.
std::string	getReferenceDatabase () const
	Returns the value of the reference_database attribute.
std::string	getReferenceDatabaseSchemaType () const
	Obtain a symbolic name for the reference_database attribute schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
std::string	getSelection () const
	Returns the value of the selection attribute.
std::string	getSelectionSchemaType () const
	Obtain a symbolic name for the selection attribute schema type.
bool	haveNumPeptides () const
	Indicates presence of the num_peptides attribute.
bool	haveReferenceAccession () const
	Indicates presence of the reference_accession attribute.
bool	haveReferenceAmount () const
	Indicates presence of the reference_amount attribute.
bool	haveReferenceDatabase () const
	Indicates presence of the reference_database attribute.
bool	haveSelection () const
	Indicates presence of the selection attribute.
ms_quant_average &	operator= (const ms_quant_average &right)
	C++ style assignment operator.
void	setNumPeptides (int value)
	Set a custom value for the num_peptides attribute.
void	setReferenceAccession (const char *value)
	Set a custom value for the reference_accession attribute.
void	setReferenceAmount (const char *value)
	Set a custom value for the reference_amount attribute.
void	setReferenceDatabase (const char *value)
	Set a custom value for the reference_database attribute.
void	setSelection (const char *value)
	Set a custom value for the selection attribute.
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 "average" element in quantitation.xml.

Serves as a possible sub-element of the "protocol" element.

Constructor & Destructor Documentation

ms_quant_average() [1/2]

ms_quant_average

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_average() [2/2]

ms_quant_average

(

const ms_quant_average &

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_average *

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.

dropNumPeptides()

void dropNumPeptides

(

)

Delete the num_peptides attribute.

Disables the attribute until it is re-set.

dropReferenceAccession()

void dropReferenceAccession

(

)

Delete the reference_accession attribute.

Disables the attribute until it is re-set.

dropReferenceAmount()

void dropReferenceAmount

(

)

Delete the reference_amount attribute.

Disables the attribute until it is re-set.

dropReferenceDatabase()

void dropReferenceDatabase

(

)

Delete the reference_database attribute.

Disables the attribute until it is re-set.

dropSelection()

void dropSelection

(

)

Delete the selection attribute.

Disables the attribute until it is re-set.

getNumberOfParameters()

int getNumberOfParameters ( ) const

virtualinherited

Returns the number of parameters held.

Returns

total number of parameters in the list.

Implements ms_xml_parameters.

getNumPeptides()

int getNumPeptides

(

)

const

Returns the value of the num_peptides attribute.

Number of peptides per protein to be used for quantitation.

Returns

current value of "num_peptides" attribute.

getNumPeptidesSchemaType()

std::string getNumPeptidesSchemaType

(

)

const

Obtain a symbolic name for the num_peptides 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.

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.

getReferenceAccession()

std::string getReferenceAccession

(

)

const

Returns the value of the reference_accession attribute.

Database accession for reference protein.

Returns

current value of the "reference_accession" attribute.

getReferenceAccessionSchemaType()

std::string getReferenceAccessionSchemaType

(

)

const

Obtain a symbolic name for the reference_accession 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.

getReferenceAmount()

std::string getReferenceAmount

(

)

const

Returns the value of the reference_amount attribute.

Amount of reference protein.

Returns

current value of the "reference_amount" attribute.

getReferenceAmountSchemaType()

std::string getReferenceAmountSchemaType

(

)

const

Obtain a symbolic name for the reference_amount 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.

getReferenceDatabase()

std::string getReferenceDatabase

(

)

const

Returns the value of the reference_database attribute.

Database database for reference protein.

Returns

current value of the "reference_database" attribute.

getReferenceDatabaseSchemaType()

std::string getReferenceDatabaseSchemaType

(

)

const

Obtain a symbolic name for the reference_database 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.

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.

getSelection()

std::string getSelection

(

)

const

Returns the value of the selection attribute.

Whether to require the peptides to be used for quantitation to be unique sequences, or to accept different modification states of same sequence (unique_mr), or even accept peptides with same sequence and modifications in different charge states (unique_mz).

Returns

current value of the "selection" attribute.

getSelectionSchemaType()

std::string getSelectionSchemaType

(

)

const

Obtain a symbolic name for the selection 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.

haveNumPeptides()

bool haveNumPeptides

(

)

const

Indicates presence of the num_peptides 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.

haveReferenceAccession()

bool haveReferenceAccession

(

)

const

Indicates presence of the reference_accession 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.

haveReferenceAmount()

bool haveReferenceAmount

(

)

const

Indicates presence of the reference_amount 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.

haveReferenceDatabase()

bool haveReferenceDatabase

(

)

const

Indicates presence of the reference_database 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.

haveSelection()

bool haveSelection

(

)

const

Indicates presence of the selection 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.

operator=()

ms_quant_average & operator=

(

const ms_quant_average &

right

)

C++ style assignment operator.

Parameters

right

another instance of this class to copy the content from.

Returns

reference to the current object

setNumPeptides()

void setNumPeptides

(

int

value

)

Set a custom value for the num_peptides attribute.

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

Parameters

value

a new value for the attribute.

setReferenceAccession()

void setReferenceAccession

(

const char *

value

)

Set a custom value for the reference_accession attribute.

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

Parameters

value

a new value for the attribute.

setReferenceAmount()

void setReferenceAmount

(

const char *

value

)

Set a custom value for the reference_amount attribute.

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

Parameters

value

a new value for the attribute.

setReferenceDatabase()

void setReferenceDatabase

(

const char *

value

)

Set a custom value for the reference_database attribute.

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

Parameters

value

a new value for the attribute.

setSelection()

void setSelection

(

const char *

value

)

Set a custom value for the selection attribute.

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

Parameters

value

a new value for the attribute.

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_average.hpp
• ms_quant_average.cpp