ms_crosslinking_linker Class Reference [Mascot configuration files module]

Linker element in crosslinking.xml More...

#include <ms_crosslinking_linker.hpp>

List of all members.

Public Member Functions
	ms_crosslinking_linker ()
	Default constructor.
	ms_crosslinking_linker (const ms_crosslinking_linker &src)
	Copying constructor.
virtual	~ms_crosslinking_linker ()
	Destructor.
void	appendDoesNotPairWith (const ms_crosslinking_does_not_pair_with *item)
	Adds a new does_not_pair_with restriction at the end of the list.
void	appendMonoLink (const ms_crosslinking_monolink *item)
	Adds a new monolink code at the end of the list.
void	clearDoesNotPairWiths ()
	Deletes all does_not_pair_with restrictions from the list.
void	clearMonoLinks ()
	Deletes all monolink codes from the list.
void	copyFrom (const ms_crosslinking_linker *right)
	Copies all content from another instance.
void	defaultValues ()
	Call this member if you want to start again.
bool	deleteDoesNotPairWithByNumber (const int idx)
	Remove a does_not_pair_with restriction from the list in memory by its index.
bool	deleteMonoLinkByNumber (const int idx)
	Remove a monolink code from the list in memory by its index.
void	dropModFileName ()
	Delete the ModFileName attribute.
const ms_crosslinking_does_not_pair_with *	getDoesNotPairWithByNumber (const int idx) const
	Returns a does_not_pair_with restriction object by its number.
std::string	getDoesNotPairWithSchemaType () const
	Obtain a symbolic name for the does_not_pair_with element schema type.
std::string	getModFileName () const
	Returns the value of the ModFileName attribute.
std::string	getModFileNameSchemaType () const
	Obtain a symbolic name for the ModFileName attribute schema type.
const ms_crosslinking_monolink *	getMonoLinkByNumber (const int idx) const
	Returns a monolink code object by its number.
std::string	getMonoLinkSchemaType () const
	Obtain a symbolic name for the monolink element schema type.
int	getNumberOfDoesNotPairWiths () const
	Returns the number of does_not_pair_with restrictions.
int	getNumberOfMonoLinks () const
	Returns the number of monolink codes.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
bool	haveModFileName () const
	Indicates presence of the ModFileName attribute.
ms_crosslinking_linker &	operator= (const ms_crosslinking_linker &right)
	C++ style assignment operator.
void	setModFileName (const char *value)
	Set a custom value for the ModFileName attribute.
bool	updateDoesNotPairWithByNumber (const int idx, const ms_crosslinking_does_not_pair_with *does_not_pair_with)
	Update the information for a specific does_not_pair_with restriction refering to it by its index.
bool	updateMonoLinkByNumber (const int idx, const ms_crosslinking_monolink *monolink)
	Update the information for a specific monolink code 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

Linker element in crosslinking.xml

The linker element specifies the modfile-style name of the linker molecule. A modfile-style name consists of the Unimod title of the linker (like "Xlink:DSS") followed by a specificity (like "Protein N-term"), e.g. "Xlink:DSS (Protein N-term)".

The linker element may list monolink definitions that should be tried as variable modifications during the search. Each monolink node is a one-letter code that identifies a "neutral loss" element in its definition.

The linker element may list does_not_pair_with restrictions. If there are no restrictions, the linker may pair with any other linker in the method. Otherwise, does_not_pair_with can be used to restrict the pairings.

---

Constructor & Destructor Documentation

ms_crosslinking_linker

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_crosslinking_linker

(

const ms_crosslinking_linker &

src )

Copying constructor.

Parameters:

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

---

Member Function Documentation

void appendDoesNotPairWith

(

const ms_crosslinking_does_not_pair_with *

item )

Adds a new does_not_pair_with restriction at the end of the list.

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

Parameters:

item	an instance of a does_not_pair_with object to copy content from.

void appendMonoLink

(

const ms_crosslinking_monolink *

item )

Adds a new monolink code at the end of the list.

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

Parameters:

item	an instance of a monolink object to copy content from.

void copyFrom

(

const ms_crosslinking_linker *

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 deleteDoesNotPairWithByNumber

(

const int

idx )

Remove a does_not_pair_with restriction from the list in memory by its index.

Parameters:

idx	number of the does_not_pair_with restriction for deletion from 0 to (getNumberOfDoesNotPairWiths() - 1).

Returns:

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

bool deleteMonoLinkByNumber

(

const int

idx )

Remove a monolink code from the list in memory by its index.

Parameters:

idx	number of the monolink code for deletion from 0 to (getNumberOfMonoLinks() - 1).

Returns:

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

void dropModFileName

(

)

Delete the ModFileName attribute.

Deletes the attribute until it is re-set.

const ms_crosslinking_does_not_pair_with * getDoesNotPairWithByNumber

(

const int

idx )

const

Returns a does_not_pair_with restriction object by its number.

Parameters:

idx	number of the does_not_pair_with restriction from 0 to (getNumberOfDoesNotPairWiths() - 1).

Returns:

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

std::string getDoesNotPairWithSchemaType

(

)

const

Obtain a symbolic name for the does_not_pair_with 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 getModFileName

(

)

const

Returns the value of the ModFileName attribute.

Returns:

a descriptive name that will appear in drop down lists, etc.

std::string getModFileNameSchemaType

(

)

const

Obtain a symbolic name for the ModFileName 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.

const ms_crosslinking_monolink * getMonoLinkByNumber

(

const int

idx )

const

Returns a monolink code object by its number.

Parameters:

idx	number of the monolink code from 0 to (getNumberOfMonoLinks() - 1).

Returns:

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

std::string getMonoLinkSchemaType

(

)

const

Obtain a symbolic name for the monolink 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 getNumberOfDoesNotPairWiths

(

)

const

Returns the number of does_not_pair_with restrictions.

Returns:

total number of does_not_pair_with restrictions.

int getNumberOfMonoLinks

(

)

const

Returns the number of monolink codes.

Returns:

total number of monolink codes.

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")

bool haveModFileName

(

)

const

Indicates presence of the ModFileName attribute.

Returns:

TRUE if the attribute is present and FALSE otherwise.

ms_crosslinking_linker & operator=

(

const ms_crosslinking_linker &

right )

C++ style assignment operator.

Parameters:

right

another instance of this class to copy the content from.

Returns:

reference to the current object

void setModFileName

(

const char *

value )

Set a custom value for the ModFileName attribute.

Parameters:

value

a new value for the attribute.

bool updateDoesNotPairWithByNumber	(	const int	idx,
		const ms_crosslinking_does_not_pair_with *	does_not_pair_with
	)

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

Parameters:

idx	number of the does_not_pair_with restriction for updating from 0 to (getNumberOfDoesNotPairWiths() - 1).
does_not_pair_with	an object to copy the content from.

Returns:

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

bool updateMonoLinkByNumber	(	const int	idx,
		const ms_crosslinking_monolink *	monolink
	)

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

Parameters:

idx	number of the monolink code for updating from 0 to (getNumberOfMonoLinks() - 1).
monolink	an object to copy the content from.

Returns:

TRUE if the monolink code has been found and 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.

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

• ms_crosslinking_linker.hpp
• ms_crosslinking_linker.cpp