ms_quant_modgroup Class Reference

An object of this class represent a single modification group element in quantitation.xml. More...

#include <ms_quant_modgroup.hpp>

Inherits ms_xml_IValidatable.

Public Member Functions
	ms_quant_modgroup ()
	Default constructor.
	ms_quant_modgroup (const ms_quant_modgroup &src)
	Copying constructor.
virtual	~ms_quant_modgroup ()
	Destructor.
void	appendLocalDefinition (const ms_quant_localdef *localdef)
	Adds a new local_definition element at the end of the list.
void	appendModFile (const char *mod)
	Adds a new mod_file at the end of the list.
void	appendUnmodified (const ms_quant_unmodified *unmodified)
	Adds a new unmodified element at the end of the list.
void	clearLocalDefinitions ()
	Deletes all local_definition elements from the list.
void	clearModFiles ()
	Deletes all mod_file elements from the list.
void	clearUnmodified ()
	Deletes all unmodified elements from the list.
void	copyFrom (const ms_quant_modgroup *right)
	Copies all content from another instance.
void	defaultValues ()
	Call this member if you want to start again.
bool	deleteLocalDefinition (const int idx)
	Removes a local_definition element from the list.
bool	deleteModFile (const int idx)
	Removes mod_file element from the list.
bool	deleteUnmodified (const int idx)
	Removes an unmodified element from the list.
void	dropMode ()
	Delete the mode attribute.
void	dropName ()
	Delete the name attribute.
void	dropRequired ()
	Delete the required attribute.
int	findModFile (const char *mod) const
	Return zero-based index of a mod_file if it is found in the list, -1 otherwise.
const ms_quant_localdef *	getLocalDefinition (const int idx) const
	Returns a local_definition element object by its number.
std::string	getLocalDefinitionSchemaType () const
	Obtain a symbolic name for the local_definition element schema type.
std::string	getMode () const
	Returns the value of the mode attribute.
std::string	getModeSchemaType () const
	Obtain a symbolic name for the mode attribute schema type.
std::string	getModFile (const int idx) const
	Returns mod_file element content by its number.
std::string	getModFileSchemaType () const
	Obtain a symbolic name for the mod_file 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.
int	getNumberOfLocalDefinitions () const
	Returns the number of nested local_definition elements.
int	getNumberOfModFiles () const
	Returns the number of nested mod_file elements.
int	getNumberOfUnmodified () const
	Returns the number of nested unmodified elements.
std::string	getRequiredSchemaType () const
	Obtain a symbolic name for the required attribute schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
const ms_quant_unmodified *	getUnmodified (const int idx) const
	Returns an unmodified element object by its number.
std::string	getUnmodifiedSchemaType () const
	Obtain a symbolic name for the unmodified element schema type.
bool	haveMode () const
	Indicates presence of the mode attribute.
bool	haveName () const
	Check for presence of the name attribute.
bool	haveRequired () const
	Indicates presence of the required attribute.
bool	isRequired () const
	Returns the value of the required attribute.
ms_quant_modgroup &	operator= (const ms_quant_modgroup &right)
	C++ style assignment operator.
void	setMode (const char *value)
	Set a custom value for the mode attribute.
void	setName (const char *value)
	Set a custom value for the name attribute.
void	setRequired (bool value)
	Set a custom value for the required attribute.
bool	updateLocalDefinition (const int idx, const ms_quant_localdef *localdef)
	Supply new content for one of the local_definition elements in the list.
bool	updateUnmodified (const int idx, const ms_quant_unmodified *unmodified)
	Supply new content for one of the unmodified elements in the list.
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 modification group element in quantitation.xml.

Grouping to enable mode constraint (e.g. exclusive) to apply to a set of modifications.

Constructor & Destructor Documentation

ms_quant_modgroup() [1/2]

ms_quant_modgroup

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_modgroup() [2/2]

ms_quant_modgroup

(

const ms_quant_modgroup &

src

)

Copying constructor.

Parameters

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

Member Function Documentation

appendLocalDefinition()

void appendLocalDefinition

(

const ms_quant_localdef *

localdef

)

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

Parameters

localdef

a new element to be added to the list.

appendModFile()

void appendModFile

(

const char *

mod

)

Adds a new mod_file at the end of the list.

Parameters

mod	a title from the Mascot mod_file.

appendUnmodified()

void appendUnmodified

(

const ms_quant_unmodified *

unmodified

)

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

Parameters

unmodified

a new element to be added to the list.

copyFrom()

void copyFrom

(

const ms_quant_modgroup *

right

)

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.

deleteLocalDefinition()

bool deleteLocalDefinition

(

const int

idx

)

Removes a local_definition element from the list.

Parameters

idx	a zero based index of the local_definition element to delete from the list.

Returns

true if the index is in rage, false otherwise

deleteModFile()

bool deleteModFile

(

const int

idx

)

Removes mod_file element from the list.

Parameters

idx	zero based index of the element to remove.

Returns

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

deleteUnmodified()

bool deleteUnmodified

(

const int

idx

)

Removes an unmodified element from the list.

Parameters

idx	a zero based index of the unmodified element to delete from the list.

Returns

true if the index is in range, false otherwise

dropMode()

void dropMode

(

)

Delete the mode attribute.

Disables the attribute until it is re-set.

dropName()

void dropName

(

)

Delete the name attribute.

Deletes the attribute until it is re-set.

dropRequired()

void dropRequired

(

)

Delete the required attribute.

Disables the attribute until it is re-set.

findModFile()

int findModFile

(

const char *

mod

)

const

Return zero-based index of a mod_file if it is found in the list, -1 otherwise.

Parameters

mod	a title from the Mascot mod_file.

Returns

zero-based index of a mod_file if it is found in the list, otherwise -1.

getLocalDefinition()

const ms_quant_localdef * getLocalDefinition

(

const int

idx

)

const

Returns a local_definition 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.

getLocalDefinitionSchemaType()

std::string getLocalDefinitionSchemaType

(

)

const

Obtain a symbolic name for the local_definition 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.

getMode()

std::string getMode

(

)

const

Returns the value of the mode attribute.

"Mode" is one of fixed, variable or exclusive. Applies to all the modifications in the group.

Returns

current value of the mode attribute.

getModeSchemaType()

std::string getModeSchemaType

(

)

const

Obtain a symbolic name for the mode 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.

getModFile()

std::string getModFile

(

const int

idx

)

const

Returns mod_file element content by its number.

Parameters

idx	zero based index of the mod_file element.

Returns

mod_file element content.

getModFileSchemaType()

std::string getModFileSchemaType

(

)

const

Obtain a symbolic name for the mod_file 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.

getName()

std::string getName

(

)

const

Returns the value of the name attribute.

Returns

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

getNameSchemaType()

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.

getNumberOfLocalDefinitions()

int getNumberOfLocalDefinitions

(

)

const

Returns the number of nested local_definition elements.

Returns

total number of nested local_definition elements.

getNumberOfModFiles()

int getNumberOfModFiles

(

)

const

Returns the number of nested mod_file elements.

Returns

total number of nested mod_file elements.

getNumberOfUnmodified()

int getNumberOfUnmodified

(

)

const

Returns the number of nested unmodified elements.

Returns

total number of nested unmodified elements.

getRequiredSchemaType()

std::string getRequiredSchemaType

(

)

const

Obtain a symbolic name for the required 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").

getUnmodified()

const ms_quant_unmodified * getUnmodified

(

const int

idx

)

const

Returns an unmodified 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.

getUnmodifiedSchemaType()

std::string getUnmodifiedSchemaType

(

)

const

Obtain a symbolic name for the unmodified 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.

haveMode()

bool haveMode

(

)

const

Indicates presence of the mode 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.

haveName()

bool haveName

(

)

const

Check for presence of the name attribute.

Returns

TRUE if the attribute is present and FALSE otherwise.

haveRequired()

bool haveRequired

(

)

const

Indicates presence of the required 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.

isRequired()

bool isRequired

(

)

const

Returns the value of the required attribute.

Modification required for a peptide to be part of a component. Does not affect the Mascot search.

Returns

current value of the required attribute.

operator=()

ms_quant_modgroup & operator=

(

const ms_quant_modgroup &

right

)

C++ style assignment operator.

Parameters

right

another instance of this class to copy the content from.

Returns

reference to the current object

setMode()

void setMode

(

const char *

value

)

Set a custom value for the mode attribute.

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

Parameters

value

a new value for the attribute.

setName()

void setName

(

const char *

value

)

Set a custom value for the name attribute.

Parameters

value

a new value for the attribute.

setRequired()

void setRequired

(

bool

value

)

Set a custom value for the required attribute.

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

Parameters

value

a new value for the attribute.

updateLocalDefinition()

bool updateLocalDefinition	(	const int	idx,
		const ms_quant_localdef *	localdef
	)

Supply new content for one of the local_definition elements in the list.

Parameters

idx	a zero based index of the element to update.
localdef	a source to copy the content from.

Returns

TRUE if the element has been successfully updated.

updateUnmodified()

bool updateUnmodified	(	const int	idx,
		const ms_quant_unmodified *	unmodified
	)

Supply new content for one of the unmodified elements in the list.

Parameters

idx	a zero based index of the element to update.
unmodified	a source to copy the content from.

Returns

TRUE if the element has been successfully updated.

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_modgroup.hpp
• ms_quant_modgroup.cpp