ms_crosslinking_method Class Reference [Mascot configuration files module]

Represents a method object in crosslinking.xml More...

#include <ms_crosslinking_method.hpp>

Collaboration diagram for ms_crosslinking_method:

List of all members.

Public Member Functions
	ms_crosslinking_method ()
	Default constructor.
	ms_crosslinking_method (const ms_crosslinking_method &src)
	Copying constructor.
virtual	~ms_crosslinking_method ()
	Destructor.
void	copyFrom (const ms_crosslinking_method *right)
	Copies all content from another instance.
void	defaultValues ()
	Call this member if you want to start again.
void	dropAccessions ()
	Delete the accessions element.
void	dropDescription ()
	Delete the description attribute.
void	dropFilters ()
	Delete the filters element.
void	dropLinkers ()
	Delete the linkers element.
void	dropName ()
	Delete the name attribute.
void	dropScope ()
	Delete the scope element.
void	dropSettings ()
	Delete the settings element.
void	dropStrategy ()
	Delete the strategy attribute.
const ms_crosslinking_accessions *	getAccessions () const
	Returns a pointer to the accessions element.
std::string	getAccessionsSchemaType () const
	Obtain a symbolic name for the accessions element schema type.
std::string	getDescription () const
	Returns the value of the description attribute.
std::string	getDescriptionSchemaType () const
	Obtain a symbolic name for the description attribute schema type.
const ms_crosslinking_filters *	getFilters () const
	Returns a pointer to the filters element.
std::string	getFiltersSchemaType () const
	Obtain a symbolic name for the filters element schema type.
const ms_crosslinking_linkers *	getLinkers () const
	Returns a pointer to the linkers element.
std::string	getLinkersSchemaType () const
	Obtain a symbolic name for the linkers element schema type.
std::string	getName () const
	Returns the value of the name attribute.
std::string	getNameSchemaType () const
	Obtain a symbolic name for the "name attribute" schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
const ms_crosslinking_scope *	getScope () const
	Returns a pointer to the scope element.
std::string	getScopeSchemaType () const
	Obtain a symbolic name for the scope element schema type.
const ms_crosslinking_settings *	getSettings () const
	Returns a pointer to the settings element.
std::string	getSettingsSchemaType () const
	Obtain a symbolic name for the settings element schema type.
std::string	getStrategy () const
	Returns the value of the strategy attribute.
std::string	getStrategySchemaType () const
	Obtain a symbolic name for the strategy attribute schema type.
bool	haveAccessions () const
	Returns TRUE if a accessions element exists.
bool	haveDescription () const
	Indicates whether the description attribute is present.
bool	haveFilters () const
	Returns TRUE if a filters element exists.
bool	haveLinkers () const
	Returns TRUE if a linkers element exists.
bool	haveName () const
	Indicates whether the name attribute is present.
bool	haveScope () const
	Returns TRUE if a scope element exists.
bool	haveSettings () const
	Returns TRUE if a settings element exists.
bool	haveStrategy () const
	Indicates whether the strategy attribute is present.
ms_crosslinking_method &	operator= (const ms_crosslinking_method &right)
	C++ style assignment operator.
void	setAccessions (const ms_crosslinking_accessions *accessions)
	Supply custom content for the accessions element.
void	setDescription (const char *value)
	Set a custom value for the description attribute.
void	setFilters (const ms_crosslinking_filters *filters)
	Supply custom content for the filters element.
void	setLinkers (const ms_crosslinking_linkers *linkers)
	Supply custom content for the linkers element.
void	setName (const char *value)
	Set a custom value for the name attribute.
void	setScope (const ms_crosslinking_scope *scope)
	Supply custom content for the scope element.
void	setSettings (const ms_crosslinking_settings *settings)
	Supply custom content for the settings element.
void	setStrategy (const char *value)
	Set a custom value for the strategy attribute.
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 a method object in crosslinking.xml

A crosslinking method is a set of parameters that define and constrain the search space. See Crosslinked search results for a full description.

---

Constructor & Destructor Documentation

ms_crosslinking_method

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_crosslinking_method

(

const ms_crosslinking_method &

src )

Copying constructor.

Parameters:

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

---

Member Function Documentation

void copyFrom

(

const ms_crosslinking_method *

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.

void dropAccessions

(

)

Delete the accessions element.

Deletes the element until it is re-set.

void dropDescription

(

)

Delete the description attribute.

Deletes the attribute until it is re-set.

void dropFilters

(

)

Delete the filters element.

Deletes the element until it is re-set.

void dropLinkers

(

)

Delete the linkers element.

Deletes the element until it is re-set.

void dropName

(

)

Delete the name attribute.

Deletes the attribute until it is re-set.

void dropScope

(

)

Delete the scope element.

Deletes the element until it is re-set.

void dropSettings

(

)

Delete the settings element.

Deletes the element until it is re-set.

void dropStrategy

(

)

Delete the strategy attribute.

Deletes the attribute until it is re-set.

const ms_crosslinking_accessions * getAccessions

(

)

const

Returns a pointer to the accessions element.

Returns:

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

std::string getAccessionsSchemaType

(

)

const

Obtain a symbolic name for the accessions 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 getDescription

(

)

const

Returns the value of the description attribute.

Returns:

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

std::string getDescriptionSchemaType

(

)

const

Obtain a symbolic name for the description attribute schema type.

The obtained type description can be used to get a corresponding type description object from ms_xml_schema.

Returns:

symbolic type description for the element.

const ms_crosslinking_filters * getFilters

(

)

const

Returns a pointer to the filters element.

Returns:

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

std::string getFiltersSchemaType

(

)

const

Obtain a symbolic name for the filters 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_crosslinking_linkers * getLinkers

(

)

const

Returns a pointer to the linkers element.

Returns:

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

std::string getLinkersSchemaType

(

)

const

Obtain a symbolic name for the linkers 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 getName

(

)

const

Returns the value of the name attribute.

Returns:

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

std::string getNameSchemaType

(

)

const

Obtain a symbolic name for the "name 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")

const ms_crosslinking_scope * getScope

(

)

const

Returns a pointer to the scope element.

Returns:

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

std::string getScopeSchemaType

(

)

const

Obtain a symbolic name for the scope 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_crosslinking_settings * getSettings

(

)

const

Returns a pointer to the settings element.

Returns:

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

std::string getSettingsSchemaType

(

)

const

Obtain a symbolic name for the settings 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 getStrategy

(

)

const

Returns the value of the strategy attribute.

Returns:

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

std::string getStrategySchemaType

(

)

const

Obtain a symbolic name for the strategy attribute schema type.

The obtained type strategy can be used to get a corresponding type description object from ms_xml_schema.

Returns:

symbolic type strategy for the element.

bool haveAccessions

(

)

const

Returns TRUE if a accessions element exists.

Returns:

TRUE if the element is present and FALSE otherwise.

bool haveDescription

(

)

const

Indicates whether the description attribute is present.

Returns:

TRUE if the attribute is present and FALSE otherwise.

bool haveFilters

(

)

const

Returns TRUE if a filters element exists.

Returns:

TRUE if the element is present and FALSE otherwise.

bool haveLinkers

(

)

const

Returns TRUE if a linkers element exists.

Returns:

TRUE if the element is present and FALSE otherwise.

bool haveName

(

)

const

Indicates whether the name attribute is present.

Returns:

TRUE if the attribute is present and FALSE otherwise.

bool haveScope

(

)

const

Returns TRUE if a scope element exists.

Returns:

TRUE if the element is present and FALSE otherwise.

bool haveSettings

(

)

const

Returns TRUE if a settings element exists.

Returns:

TRUE if the element is present and FALSE otherwise.

bool haveStrategy

(

)

const

Indicates whether the strategy attribute is present.

Returns:

TRUE if the attribute is present and FALSE otherwise.

ms_crosslinking_method & operator=

(

const ms_crosslinking_method &

right )

C++ style assignment operator.

Parameters:

right

another instance of this class to copy the content from.

Returns:

reference to the current object

void setAccessions

(

const ms_crosslinking_accessions *

accessions )

Supply custom content for the accessions element.

Parameters:

accessions

a new content for the element.

void setDescription

(

const char *

value )

Set a custom value for the description attribute.

Parameters:

value

a new value for the attribute.

void setFilters

(

const ms_crosslinking_filters *

filters )

Supply custom content for the filters element.

Parameters:

filters

a new content for the element.

void setLinkers

(

const ms_crosslinking_linkers *

linkers )

Supply custom content for the linkers element.

Parameters:

linkers

a new content for the element.

void setName

(

const char *

value )

Set a custom value for the name attribute.

Parameters:

value

a new value for the attribute.

void setScope

(

const ms_crosslinking_scope *

scope )

Supply custom content for the scope element.

Parameters:

scope

a new content for the element.

void setSettings

(

const ms_crosslinking_settings *

settings )

Supply custom content for the settings element.

Parameters:

settings

a new content for the element.

void setStrategy

(

const char *

value )

Set a custom value for the strategy attribute.

Parameters:

value

a new value for the attribute.

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_method.hpp
• ms_crosslinking_method.cpp