ms_quant_precursor Class Reference [Mascot configuration files module]

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

#include <ms_quant_precursor.hpp>

Inheritance diagram for ms_quant_precursor:

Collaboration diagram for ms_quant_precursor:

List of all members.

Public Member Functions
	ms_quant_precursor ()
	Default constructor.
	ms_quant_precursor (const ms_quant_precursor &src)
	Copying constructor.
virtual	~ms_quant_precursor ()
	Destructor.
void	appendParameter (const ms_quant_parameter *item)
	Adds a new parameter at the end of the list.
virtual void	clearParameters ()
	Deletes all parameters from the list.
void	copyFrom (const ms_quant_precursor *right)
	Copies all content from another instance.
void	copyFrom (const ms_quant_parameters *right)
	Copies all content from another instance.
void	defaultValues ()
	Call this member if you want to start again.
virtual bool	deleteParameterByName (const char *name)
	Remove a parameter from the list in memory by its unique name.
virtual bool	deleteParameterByNumber (const int idx)
	Remove a parameter from the list in memory by its index.
void	dropAllChargeStates ()
void	dropAllowElutionShift ()
void	dropAllowMassTimeMatch ()
	Delete the allow_mass_time_match attribute.
std::string	getAllChargeStatesSchemaType () const
std::string	getAllowElutionShiftSchemaType () const
std::string	getAllowMassTimeMatchSchemaType () const
	Obtain a symbolic name for the allow_mass_time_match attribute schema type.
virtual int	getNumberOfParameters () const
	Returns the number of parameters held.
const ms_quant_parameter *	getParameterByName (const char *name) const
	Returns a parameter object by its name or a null value in case of not found.
const ms_quant_parameter *	getParameterByNumber (const int idx) const
	Returns a parameter object by its number.
virtual std::string	getParameterSchemaType () const
	Obtain a symbolic name for the parameter element schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
bool	haveAllChargeStates () const
bool	haveAllowElutionShift () const
bool	haveAllowMassTimeMatch () const
	Indicates presence of the allow_mass_time_match attribute.
bool	isAllChargeStates () const
bool	isAllowElutionShift () const
bool	isAllowMassTimeMatch () const
	Returns the value of the allow_mass_time_match attribute.
ms_quant_precursor &	operator= (const ms_quant_precursor &right)
	C++ style assignment operator.
void	setAllowMassTimeMatch (const bool value)
	Set a custom value for the allow_mass_time_match attribute.
bool	updateParameterByName (const char *name, const ms_quant_parameter *param)
	Update the information for a specific parameter refering to it by its unique name.
bool	updateParameterByNumber (const int idx, const ms_quant_parameter *param)
	Update the information for a specific parameter 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.

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Detailed Description

An object of this class represent a single precursor element in quantitation.xml.

Serves as a possible sub-element of "protocol" element

---

Constructor & Destructor Documentation

ms_quant_precursor

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_precursor

(

const ms_quant_precursor &

src )

Copying constructor.

Parameters:

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

---

Member Function Documentation

void appendParameter

(

const ms_quant_parameter *

item )

[inherited]

Adds a new parameter at the end of the list.

Parameters:

item	an instance of parameter object to copy content from.

void copyFrom

(

const ms_quant_precursor *

right )

Copies all content from another instance.

Parameters:

right

another instance of this class to copy the content from.

void copyFrom

(

const ms_quant_parameters *

right )

[inherited]

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.

Reimplemented from ms_quant_parameters.

bool deleteParameterByName

(

const char *

name )

[virtual, inherited]

Remove a parameter from the list in memory by its unique name.

Parameters:

name	name of the parameter for deletion.

Returns:

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

Implements ms_xml_parameters.

bool deleteParameterByNumber

(

const int

idx )

[virtual, inherited]

Remove a parameter from the list in memory by its index.

Parameters:

idx	number of the parameter for deletion from 0 to (getNumberOfParameters() - 1).

Returns:

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

Implements ms_xml_parameters.

void dropAllChargeStates

(

)

Deprecated:

Moved to ms_quant_integration.

This function is no longer available in Parser 2.3 See ms_quant_integration::setAllChargeStates(). param value new value

Deprecated:

Moved to ms_quant_integration.

void dropAllowElutionShift

(

)

Deprecated:

Moved to ms_quant_integration.

This function is no longer available in Parser 2.3 See ms_quant_integration::setAllowElutionShift(). param value new value

Deprecated:

Moved to ms_quant_integration.

void dropAllowMassTimeMatch

(

)

Delete the allow_mass_time_match attribute.

Disables the attribute until it is re-set.

std::string getAllChargeStatesSchemaType

(

)

const

Deprecated:

Moved to ms_quant_integration.

Returns:

all charge states schema type

std::string getAllowElutionShiftSchemaType

(

)

const

Deprecated:

Moved to ms_quant_integration.

Returns:

allow elution shift schema type

std::string getAllowMassTimeMatchSchemaType

(

)

const

Obtain a symbolic name for the allow_mass_time_match 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 getNumberOfParameters

(

)

const [virtual, inherited]

Returns the number of parameters held.

Returns:

total number of parameters in the list.

Implements ms_xml_parameters.

const ms_quant_parameter * getParameterByName

(

const char *

name )

const [inherited]

Returns a parameter object by its name or a null value in case of not found.

Parameters:

name	name of the parameter to find.

Returns:

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

const ms_quant_parameter * getParameterByNumber

(

const int

idx )

const [inherited]

Returns a parameter object by its number.

Parameters:

idx	number of the parameter from 0 to (getNumberOfParameters() - 1).

Returns:

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

std::string getParameterSchemaType

(

)

const [virtual, inherited]

Obtain a symbolic name for the parameter 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.

Implements ms_xml_parameters.

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").

Reimplemented from ms_quant_parameters.

bool haveAllChargeStates

(

)

const

Deprecated:

Moved to ms_quant_integration.

Returns:

true if all charge states is set, false otherwise

bool haveAllowElutionShift

(

)

const

Deprecated:

Moved to ms_quant_integration.

Returns:

true if allow elution shift is set, false otherwise

bool haveAllowMassTimeMatch

(

)

const

Indicates presence of the allow_mass_time_match 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.

bool isAllChargeStates

(

)

const

Deprecated:

Moved to ms_quant_integration.

Returns:

true if all charge states is set, false otherwise

bool isAllowElutionShift

(

)

const

Deprecated:

Moved to ms_quant_integration.

Returns:

true if allow elution shift is set, false otherwise

bool isAllowMassTimeMatch

(

)

const

Returns the value of the allow_mass_time_match attribute.

If false, we only report a ratio if we have peptide matches to both components. Also, if false, then all_charge_states treated as false, even if true in method. Almost always set true in practice.

Returns:

TRUE/FALSE.

ms_quant_precursor & operator=

(

const ms_quant_precursor &

right )

C++ style assignment operator.

Parameters:

right

another instance of this class to copy the content from.

Returns:

reference to the current object

void setAllowMassTimeMatch

(

const bool

value )

Set a custom value for the allow_mass_time_match attribute.

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

Parameters:

value

a new value for the attribute.

bool updateParameterByName	(	const char *	name,
		const ms_quant_parameter *	param
	)		[inherited]

Update the information for a specific parameter refering to it by its unique name.

Parameters:

name	name of the parameter for updating.
param	an object to copy the content from.

Returns:

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

bool updateParameterByNumber	(	const int	idx,
		const ms_quant_parameter *	param
	)		[inherited]

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

Parameters:

idx	number of the parameter for updating from 0 to (getNumberOfParameters() - 1).
param	an object to copy the content from.

Returns:

TRUE if the parameter 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.

Reimplemented from ms_xml_parameters.

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.

Reimplemented from ms_xml_parameters.

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

• ms_quant_precursor.hpp
• ms_quant_precursor.cpp