ms_umod_specificity Class Reference [Mascot configuration files module]

Represents modification specificity objects in unimod.xml. More...

#include <ms_umod_specificity.hpp>

List of all members.

Public Member Functions
	ms_umod_specificity ()
	Default constructor.
	ms_umod_specificity (const ms_umod_specificity &src)
	Copying constructor.
	ms_umod_specificity (const ms_quant_specificity &src, const ms_umod_configfile &umodFile)
	Copying constructor that takes an object from quantitation.xml.
virtual	~ms_umod_specificity ()
	Destructor.
void	appendNeutralLoss (const ms_umod_neutralloss *nl)
	Adds a new 'NeutralLoss' element at the end of the list.
void	appendPepNeutralLoss (const ms_umod_neutralloss *pnl)
	Adds a new 'PepNeutralLoss' element at the end of the list.
void	clearNeutralLosses ()
	Deletes all 'NeutralLoss' elements from the list.
void	clearPepNeutralLosses ()
	Deletes all 'PepNeutralLoss' elements from the list.
void	copyFrom (const ms_umod_specificity *right)
	Copies all content from another instance.
void	copyFrom (const ms_quant_specificity *right, const ms_umod_configfile &umodFile)
	Copies all content from an object of quantitation.xml.
void	defaultValues ()
	Call this member if you want to start again.
bool	deleteNeutralLoss (const int idx)
	Remove a 'NeutralLoss' element from the list in memory.
bool	deletePepNeutralLoss (const int idx)
	Remove a 'PepNeutralLoss' element object from the list in memory.
void	dropClassification ()
	Delete the classification attribute.
void	dropHidden ()
	Delete the hidden attribute.
void	dropMiscNotes ()
	Delete the misc_notes element.
void	dropPosition ()
	Delete the position attribute.
void	dropSite ()
	Delete the site attribute.
void	dropSpecGroup ()
	Delete the spec_group attribute.
std::string	getClassification () const
	Returns the value of the classification attribute.
std::string	getClassificationSchemaType () const
	Obtain a symbolic name for the classification attribute schema type.
std::string	getHiddenSchemaType () const
	Obtain a symbolic name for the hidden attribute schema type.
std::string	getMiscNotes () const
	Returns the value of the misc_notes element.
std::string	getMiscNotesSchemaType () const
	Obtain a symbolic name for the misc_notes element schema type.
const ms_umod_neutralloss *	getNeutralLoss (const int idx) const
	Returns a read-only pointer to a 'NeutralLoss' element 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 currently held in memory.
int	getNumberOfPepNeutralLosses () const
	Returns the number of 'PepNeutralLoss' elements currently held in memory.
const ms_umod_neutralloss *	getPepNeutralLoss (const int idx) const
	Returns a read-only pointer to a 'PepNeutralLoss' element object by its number.
std::string	getPepNeutralLossSchemaType () const
	Obtain a symbolic name for the 'NeutralLoss' 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.
int	getSpecGroup () const
	Returns the value of the spec_group attribute.
std::string	getSpecGroupSchemaType () const
	Obtain a symbolic name for the spec_group attribute schema type.
bool	haveClassification () const
	Indicates presence of the classification attribute.
bool	haveHidden () const
	Indicates presence of the hidden attribute.
bool	haveMiscNotes () const
	Indicates presence of the misc_notes element.
bool	havePosition () const
	Indicates presence of the position attribute.
bool	haveSite () const
	Indicates presence of the site attribute.
bool	haveSpecGroup () const
	Indicates presence of the spec_group attribute.
bool	inErrorTolerant () const
bool	inLongList () const
	Indicates whether this specificity is in the full list on the Mascot search form.
bool	inShortList () const
	Indicates whether this specificity is in the short list on the Mascot search form.
bool	isHidden () const
	Returns the value of the hidden attribute.
bool	isSameAs (const ms_umod_specificity &right) const
	Returns true if instances contain the same information.
ms_umod_specificity &	operator= (const ms_umod_specificity &right)
	C++ style assignment operator.
void	setClassification (const char *value)
	Set a custom value for the classification attribute.
void	setHidden (const bool value)
	Set a custom value for the hidden attribute.
void	setMiscNotes (const char *value)
	Set a custom value for the misc_notes element.
void	setPosition (const char *value)
	Set a custom value for the position attribute.
void	setSite (const char *value)
	Set a custom value for the site attribute.
void	setSpecGroup (const int value)
	Set a custom value for the spec_group attribute.
void	showInLongList (bool b)
void	showInShortList (bool b)
bool	updateNeutralLoss (const int idx, const ms_umod_neutralloss *nl)
	Update the information for a particular 'NeutralLoss' element.
bool	updatePepNeutralLoss (const int idx, const ms_umod_neutralloss *pnl)
	Update the information for a particular 'PepNeutralLoss' element.
void	useInErrorTolerant (bool b)
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

Represents modification specificity objects in unimod.xml.

---

Constructor & Destructor Documentation

ms_umod_specificity

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_umod_specificity

(

const ms_umod_specificity &

src )

Copying constructor.

Parameters:

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

ms_umod_specificity	(	const ms_quant_specificity &	src,
		const ms_umod_configfile &	umodFile
	)

Copying constructor that takes an object from quantitation.xml.

Parameters:

src	an instance of quantitation.xml class to copy the content from.
umodFile	a Unimod file object to extract element masses from.

---

Member Function Documentation

void appendNeutralLoss

(

const ms_umod_neutralloss *

nl )

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

Creates a new neutral loss object, copies all content from the object supplied as a parameter and adds it at the end of the list.

Parameters:

nl	an instance of neutral loss object to copy the content from.

void appendPepNeutralLoss

(

const ms_umod_neutralloss *

pnl )

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

Creates a new peptide neutral loss object, copies all content from the object supplied as a parameter and adds it at the end of the list.

Parameters:

pnl	an instance of peptide neutral loss object to copy the content from.

void copyFrom

(

const ms_umod_specificity *

right )

Copies all content from another instance.

Parameters:

right

another instance of this class to copy the content from.

void copyFrom	(	const ms_quant_specificity *	right,
		const ms_umod_configfile &	umodFile
	)

Copies all content from an object of quantitation.xml.

Parameters:

right	an instance of a quantitation.xml class.
umodFile	a Unimod file object to extract element masses 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 in memory.

Parameters:

idx	number of the neutral loss for deletion from 0 to (getNumberOfNeutralLosses() - 1).

Returns:

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

bool deletePepNeutralLoss

(

const int

idx )

Remove a 'PepNeutralLoss' element object from the list in memory.

Parameters:

idx	number of the peptide neutral loss for deletion from 0 to (getNumberOfPepNeutralLosses() - 1).

Returns:

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

void dropClassification

(

)

Delete the classification attribute.

Deletes the attribute until is re-set.

void dropHidden

(

)

Delete the hidden attribute.

Deletes the attribute until is re-set.

void dropMiscNotes

(

)

Delete the misc_notes element.

Deletes the element until it is re-set.

void dropPosition

(

)

Delete the position attribute.

Deletes the attribute until is re-set.

void dropSite

(

)

Delete the site attribute.

Deletes the attribute until is re-set.

void dropSpecGroup

(

)

Delete the spec_group attribute.

Deletes the attribute until is re-set.

std::string getClassification

(

)

const

Returns the value of the classification attribute.

Returns:

current value of the attribute.

std::string getClassificationSchemaType

(

)

const

Obtain a symbolic name for the classification 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 getHiddenSchemaType

(

)

const

Obtain a symbolic name for the hidden 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 getMiscNotes

(

)

const

Returns the value of the misc_notes element.

Returns:

current value of the element.

std::string getMiscNotesSchemaType

(

)

const

Obtain a symbolic name for the misc_notes 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_umod_neutralloss * getNeutralLoss

(

const int

idx )

const

Returns a read-only pointer to a 'NeutralLoss' element by its number.

Parameters:

idx	number of the neutral loss from 0 to (getNumberOfNeutralLosses() - 1).

Returns:

a read-only pointer to the retrieved object. 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.

int getNumberOfNeutralLosses

(

)

const

Returns the number of 'NeutralLoss' elements currently held in memory.

Returns:

total number of neutral losses in the specificity.

int getNumberOfPepNeutralLosses

(

)

const

Returns the number of 'PepNeutralLoss' elements currently held in memory.

Returns:

total number of peptide neutral losses in the specificity.

const ms_umod_neutralloss * getPepNeutralLoss

(

const int

idx )

const

Returns a read-only pointer to a 'PepNeutralLoss' element object by its number.

Parameters:

idx	number of the peptide neutral loss from 0 to (getNumberOfPepNeutralLosses() - 1).

Returns:

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

std::string getPepNeutralLossSchemaType

(

)

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.

std::string getPosition

(

)

const

Returns the value of the position attribute.

Returns:

Position of the specificity that should be one of the Type mqm:positionType values.

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, "umod:nameType")

std::string getSite

(

)

const

Returns the value of the site attribute.

Returns:

Site string that should be one of the Type mqm:siteType values.

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.

int getSpecGroup

(

)

const

Returns the value of the spec_group attribute.

Returns:

current value of the attribute.

std::string getSpecGroupSchemaType

(

)

const

Obtain a symbolic name for the spec_group 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 haveClassification

(

)

const

Indicates presence of the classification attribute.

Returns:

TRUE if the attribute is present and FALSE otherwise.

bool haveHidden

(

)

const

Indicates presence of the hidden attribute.

Returns:

TRUE if the attribute is present and FALSE otherwise.

bool haveMiscNotes

(

)

const

Indicates presence of the misc_notes element.

Returns:

TRUE if the element is present and FALSE otherwise.

bool havePosition

(

)

const

Indicates presence of the position attribute.

Returns:

TRUE if the attribute is present and FALSE otherwise.

bool haveSite

(

)

const

Indicates presence of the site attribute.

Returns:

TRUE if the attribute is present and FALSE otherwise.

bool haveSpecGroup

(

)

const

Indicates presence of the spec_group attribute.

Returns:

TRUE if the attribute is present and FALSE otherwise.

bool inErrorTolerant

(

)

const

Returns:

true if this specificity is included in error tolerant searches in mascot.

bool inLongList

(

)

const

Indicates whether this specificity is in the full list on the Mascot search form.

Returns:

true if this specificity is required in the mascot search form full list.

bool inShortList

(

)

const

Indicates whether this specificity is in the short list on the Mascot search form.

Returns:

true if this specificity is required in the mascot search form short list.

bool isHidden

(

)

const

Returns the value of the hidden attribute.

Returns:

current value of the attribute.

bool isSameAs

(

const ms_umod_specificity &

right )

const

Returns true if instances contain the same information.

Parameters:

right

another instance of this class to compare.

Returns:

true if the specificities are equivalent.

ms_umod_specificity & operator=

(

const ms_umod_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 setClassification

(

const char *

value )

Set a custom value for the classification attribute.

Parameters:

value

a new value for the attribute.

void setHidden

(

const bool

value )

Set a custom value for the hidden attribute.

Parameters:

value

a new value for the attribute.

void setMiscNotes

(

const char *

value )

Set a custom value for the misc_notes element.

Parameters:

value

a new value for the element.

void setPosition

(

const char *

value )

Set a custom value for the position attribute.

Parameters:

value

Position of the specificity that should be one of the Type mqm:positionType values.

void setSite

(

const char *

value )

Set a custom value for the site attribute.

Parameters:

value

that should be one of the Type mqm:siteType values.

void setSpecGroup

(

const int

value )

Set a custom value for the spec_group attribute.

Parameters:

value

a new value for the attribute.

void showInLongList

(

bool

b )

Parameters:

b	sets if this specificity is required in the mascot search form full list.

void showInShortList

(

bool

b )

Parameters:

b	sets if this specificity is required in the mascot search form short list.

bool updateNeutralLoss	(	const int	idx,
		const ms_umod_neutralloss *	nl
	)

Update the information for a particular 'NeutralLoss' element.

Parameters:

idx	number of the neutral loss object for updating from 0 to (getNumberOfNeutralLosses() - 1).
nl	an object to copy the content from.

Returns:

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

bool updatePepNeutralLoss	(	const int	idx,
		const ms_umod_neutralloss *	pnl
	)

Update the information for a particular 'PepNeutralLoss' element.

Parameters:

idx	number of the peptide neutral loss object for updating from 0 to (getNumberOfPepNeutralLosses() - 1).
pnl	an object to copy the content from.

Returns:

TRUE if the peptide neutral loss has been found and successfully updated and FALSE otherwise.

void useInErrorTolerant

(

bool

b )

Parameters:

b	sets if this specificity is required in error tolerant searches.

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_umod_specificity.hpp
• ms_umod_specificity.cpp