ms_quant_specificity Class Reference [Mascot configuration files module]

Describes a specificity element in quantitation.xml (Unimod style specificity). More...

#include <ms_quant_specificity.hpp>

List of all members.

Public Member Functions
	ms_quant_specificity ()
	Default constructor.
	ms_quant_specificity (const ms_quant_specificity &src)
	Copying constructor.
virtual	~ms_quant_specificity ()
	Destructor.
void	appendNeutralLoss (const ms_quant_neutralloss *neutralloss)
	Adds a new NeutralLoss element at the end of the list.
void	appendPepNeutralLoss (const ms_quant_pepneutralloss *neutralloss)
	Adds a new PepNeutralLoss element at the end of the list.
void	clearNeutralLosses ()
	Deletes all elements from the list.
void	clearPepNeutralLosses ()
	Deletes all elements from the list.
void	copyFrom (const ms_quant_specificity *right)
	Copies all content from another instance.
void	defaultValues ()
	Call this member if you want to start again.
bool	deleteNeutralLoss (const int idx)
	Remove a NeutralLoss element from the list.
bool	deletePepNeutralLoss (const int idx)
	Remove a PepNeutralLoss element from the list.
void	dropPosition ()
	Deletes the position attribute.
void	dropSite ()
	Deletes the site attribute.
const ms_quant_neutralloss *	getNeutralLoss (const int idx) const
	Returns a NeutralLoss element object by its number.
std::string	getNeutralLossSchemaType () const
	Obtain a symbolic name for the NeutralLoss element schema type.
int	getNumberOfNeutralLosses () const
	Returns the number of NeutralLoss elements held.
int	getNumberOfPepNeutralLosses () const
	Returns the number of PepNeutralLoss elements held.
const ms_quant_pepneutralloss *	getPepNeutralLoss (const int idx) const
	Returns a pointer to the PepNeutralLoss element by its number.
std::string	getPepNeutralLossSchemaType () const
	Obtain a symbolic name for the PepNeutralLoss element schema type.
std::string	getPosition () const
	Returns the value of the position attribute.
std::string	getPositionSchemaType () const
	Obtain a symbolic name for the position attribute schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
std::string	getSite () const
	Returns the value of the site attribute.
std::string	getSiteSchemaType () const
	Obtain a symbolic name for the site attribute schema type.
bool	havePosition () const
	Indicates whether the position attribute is present or not.
bool	haveSite () const
	Indicates whether the site attribute is present or not.
ms_quant_specificity &	operator= (const ms_quant_specificity &right)
	C++ style assignment operator.
void	setPosition (const char *position)
	Set a custom value for the position attribute.
void	setSite (const char *site)
	Set a custom value for the site attribute.
bool	updateNeutralLoss (const int idx, const ms_quant_neutralloss *neutralloss)
	Update the information for a specific neutral loss.
bool	updatePepNeutralLoss (const int idx, const ms_quant_pepneutralloss *neutralloss)
	Update the information for a specific peptide neutral loss.
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

Describes a specificity element in quantitation.xml (Unimod style specificity).

Objects of this type host a list of nested NeutralLoss elements.

---

Constructor & Destructor Documentation

ms_quant_specificity

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_specificity

(

const ms_quant_specificity &

src )

Copying constructor.

Parameters:

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

---

Member Function Documentation

void appendNeutralLoss

(

const ms_quant_neutralloss *

neutralloss )

Adds a new NeutralLoss element at the end of the list.

Parameters:

neutralloss

an instance to copy the content into the newly added element from.

void appendPepNeutralLoss

(

const ms_quant_pepneutralloss *

pepneutralloss )

Adds a new PepNeutralLoss element at the end of the list.

Parameters:

pepneutralloss

an instance to copy the content into the newly added element from.

void copyFrom

(

const ms_quant_specificity *

right )

Copies all content from another instance.

Parameters:

right

another instance of this class to copy the content from.

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.

bool deleteNeutralLoss

(

const int

idx )

Remove a NeutralLoss element from the list.

Parameters:

idx	a zero-based index of the element to delete.

Returns:

TRUE if the element has been successfully deleted and FALSE otherwise.

bool deletePepNeutralLoss

(

const int

idx )

Remove a PepNeutralLoss element from the list.

Parameters:

idx	a zero-based index of the element to delete.

Returns:

TRUE if the element has been successfully deleted and FALSE otherwise.

void dropPosition

(

)

Deletes the position attribute.

Disables the attribute until it is re-set.

void dropSite

(

)

Deletes the site attribute.

Disables the attribute until it is re-set.

const ms_quant_neutralloss * getNeutralLoss

(

const int

idx )

const

Returns a NeutralLoss element object by its number.

Parameters:

idx	a zero-based index of the element to retrieve.

Returns:

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

std::string getNeutralLossSchemaType

(

)

const

Obtain a symbolic name for the NeutralLoss 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.

const ms_quant_pepneutralloss * getPepNeutralLoss

(

const int

idx )

const

Returns a pointer to the PepNeutralLoss element by its number.

Parameters:

idx	a zero-based index of the element to obtain.

Returns:

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

std::string getPepNeutralLossSchemaType

(

)

const

Obtain a symbolic name for the PepNeutralLoss 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.

std::string getPosition

(

)

const

Returns the value of the position attribute.

Returns:

current value of the position attribute.

std::string getPositionSchemaType

(

)

const

Obtain a symbolic name for the position 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.

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").

std::string getSite

(

)

const

Returns the value of the site attribute.

Returns:

current value of the site attribute.

std::string getSiteSchemaType

(

)

const

Obtain a symbolic name for the site 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.

bool havePosition

(

)

const

Indicates whether the position attribute is present or not.

Returns:

TRUE if the attribute is available.

bool haveSite

(

)

const

Indicates whether the site attribute is present or not.

Returns:

TRUE if the attribute is available.

ms_quant_specificity & operator=

(

const ms_quant_specificity &

right )

C++ style assignment operator.

Parameters:

right

another instance of this class to copy the content from.

Returns:

reference to the current object

void setPosition

(

const char *

position )

Set a custom value for the position attribute.

Calling this method makes the attribute automatically available in the current element.

Parameters:

position

a new value for the position attribute.

void setSite

(

const char *

site )

Set a custom value for the site attribute.

Calling this method makes the attribute automatically available in the current element.

Parameters:

site	a new value for the site attribute.

bool updateNeutralLoss	(	const int	idx,
		const ms_quant_neutralloss *	neutralloss
	)

Update the information for a specific neutral loss.

Parameters:

idx	a zero-based index of the element to update.
neutralloss	an instance to copy the content from.

Returns:

TRUE if the element has been successfully updated and FALSE otherwise.

bool updatePepNeutralLoss	(	const int	idx,
		const ms_quant_pepneutralloss *	pepneutralloss
	)

Update the information for a specific peptide neutral loss.

Parameters:

idx	a zero-based index of the element to update.
pepneutralloss	an instance to copy the content from.

Returns:

TRUE if the element has been successfully updated and FALSE otherwise.

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.

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.

---

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

• ms_quant_specificity.hpp
• ms_quant_specificity.cpp