ms_quant_quality Class Reference

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

#include <ms_quant_quality.hpp>

Inheritance diagram for ms_quant_quality:

Collaboration diagram for ms_quant_quality:

Public Member Functions
	ms_quant_quality ()
	Default constructor.
	ms_quant_quality (const ms_quant_quality &src)
	Copying constructor.
virtual	~ms_quant_quality ()
	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_parameters *right)
	Copies all content from another instance.
void	copyFrom (const ms_quant_quality *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	dropIsolatedPrecursor ()
	Delete the isolated_precursor attribute.
void	dropIsolatedPrecursorThreshold ()
	Delete the isolated_precursor_threshold attribute.
void	dropMinimumA1 ()
	Delete the minimum_a1 attribute.
void	dropMinPrecursorCharge ()
	Delete the min_precursor_charge attribute.
void	dropPepThresholdType ()
	Delete the pep_threshold_type attribute.
void	dropPepThresholdValue ()
	Delete the pep_threshold_value attribute.
void	dropTotalIntensity ()
	Delete the total_intensity attribute.
void	dropTotalIntensityThreshold ()
	Delete the total_intensity_threshold attribute.
void	dropUniquePepseq ()
	Delete the unique_pepseq attribute.
std::string	getIsolatedPrecursorSchemaType () const
	Obtain a symbolic name for the isolated_precursor attribute schema type.
std::string	getIsolatedPrecursorThreshold () const
	Returns the value of the isolated_precursor_threshold attribute.
std::string	getIsolatedPrecursorThresholdSchemaType () const
	Obtain a symbolic name for the isolated_precursor_threshold attribute schema type.
std::string	getMinimumA1 () const
	Returns the value of the minimum_a1 attribute.
std::string	getMinimumA1SchemaType () const
	Obtain a symbolic name for the minimum_a1 attribute schema type.
int	getMinPrecursorCharge () const
	Returns the value of the min_precursor_charge attribute.
std::string	getMinPrecursorChargeSchemaType () const
	Obtain a symbolic name for the min_precursor_charge 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.
std::string	getPepThresholdType () const
	Returns the value of the pep_threshold_type attribute.
std::string	getPepThresholdTypeSchemaType () const
	Obtain a symbolic name for the pep_threshold_type attribute schema type.
std::string	getPepThresholdValue () const
	Returns the value of the pep_threshold_value attribute.
std::string	getPepThresholdValueSchemaType () const
	Obtain a symbolic name for the "pep_threshold_value" schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
std::string	getTotalIntensitySchemaType () const
	Obtain a symbolic name for the total_intensity attribute schema type.
std::string	getTotalIntensityThreshold () const
	Returns the value of the total_intensity_threshold attribute.
std::string	getTotalIntensityThresholdSchemaType () const
	Obtain a symbolic name for the total_intensity_threshold attribute schema type.
std::string	getUniquePepseqSchemaType () const
	Obtain a symbolic name for the unique_pepseq attribute schema type.
bool	haveIsolatedPrecursor () const
	Indicates presence of the isolated_precursor attribute.
bool	haveIsolatedPrecursorThreshold () const
	Indicates presence of the isolated_precursor_threshold attribute.
bool	haveMinimumA1 () const
	Indicates presence of the minimum_a1 attribute.
bool	haveMinPrecursorCharge () const
	Indicates presence of the min_precursor_charge attribute.
bool	havePepThresholdType () const
	Indicates presence of the pep_threshold_type attribute.
bool	havePepThresholdValue () const
	Indicates presence of the pep_threshold_value attribute.
bool	haveTotalIntensity () const
	Indicates presence of the total_intensity attribute.
bool	haveTotalIntensityThreshold () const
	Indicates presence of the total_intensity_threshold attribute.
bool	haveUniquePepseq () const
	Indicates presence of the unique_pepseq attribute.
bool	isIsolatedPrecursor () const
	Returns the value of the isolated_precursor attribute.
bool	isTotalIntensity () const
	Returns the value of the total_intensity attribute.
bool	isUniquePepseq () const
	Returns the value of the unique_pepseq attribute.
ms_quant_quality &	operator= (const ms_quant_quality &right)
	C++ style assignment operator.
void	setIsolatedPrecursor (const bool value)
	Set a custom value for the isolated_precursor attribute.
void	setIsolatedPrecursorThreshold (const char *value)
	Set a custom value for the isolated_precursor_threshold attribute.
void	setMinimumA1 (const char *value)
	Set a custom value for the minimum_a1 attribute.
void	setMinPrecursorCharge (const int value)
	Set a custom value for the min_precursor_charge attribute.
void	setPepThresholdType (const char *value)
	Set a custom value for the pep_threshold_type attribute.
void	setPepThresholdValue (const char *value)
	Set a custom value for the pep_threshold_value attribute.
void	setTotalIntensity (bool value)
	Set a custom value for the total_intensity attribute.
void	setTotalIntensityThreshold (std::string value)
	Set a custom value for the total_intensity_threshold attribute.
void	setUniquePepseq (bool value)
	Set a custom value for the unique_pepseq 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.

Detailed Description

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

Constructor & Destructor Documentation

ms_quant_quality() [1/2]

ms_quant_quality

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_quality() [2/2]

ms_quant_quality

(

const ms_quant_quality &

src

)

Copying constructor.

Parameters

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

Member Function Documentation

appendParameter()

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.

copyFrom() [1/2]

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.

copyFrom() [2/2]

void copyFrom

(

const ms_quant_quality *

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.

deleteParameterByName()

bool deleteParameterByName ( const char *  name )

virtualinherited

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.

deleteParameterByNumber()

bool deleteParameterByNumber ( const int  idx )

virtualinherited

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.

dropIsolatedPrecursor()

void dropIsolatedPrecursor

(

)

Delete the isolated_precursor attribute.

Disables the attribute until it is re-set.

dropIsolatedPrecursorThreshold()

void dropIsolatedPrecursorThreshold

(

)

Delete the isolated_precursor_threshold attribute.

Disables the attribute until it is re-set.

dropMinimumA1()

void dropMinimumA1

(

)

Delete the minimum_a1 attribute.

Disables the attribute until it is re-set.

dropMinPrecursorCharge()

void dropMinPrecursorCharge

(

)

Delete the min_precursor_charge attribute.

Disables the attribute until it is re-set.

dropPepThresholdType()

void dropPepThresholdType

(

)

Delete the pep_threshold_type attribute.

Disables the attribute until it is re-set.

dropPepThresholdValue()

void dropPepThresholdValue

(

)

Delete the pep_threshold_value attribute.

Disables the attribute until it is re-set.

dropTotalIntensity()

void dropTotalIntensity

(

)

Delete the total_intensity attribute.

Disables the attribute until it is re-set.

dropTotalIntensityThreshold()

void dropTotalIntensityThreshold

(

)

Delete the total_intensity_threshold attribute.

Disables the attribute until it is re-set.

dropUniquePepseq()

void dropUniquePepseq

(

)

Delete the unique_pepseq attribute.

Disables the attribute until it is re-set.

getIsolatedPrecursorSchemaType()

std::string getIsolatedPrecursorSchemaType

(

)

const

Obtain a symbolic name for the isolated_precursor 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.

getIsolatedPrecursorThreshold()

std::string getIsolatedPrecursorThreshold

(

)

const

Returns the value of the isolated_precursor_threshold attribute.

Threshold on the fraction of the peak area in the precursor region accounted for by the components.

Returns

current value of the isolated_precursor_threshold attribute.

getIsolatedPrecursorThresholdSchemaType()

std::string getIsolatedPrecursorThresholdSchemaType

(

)

const

Obtain a symbolic name for the isolated_precursor_threshold 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.

getMinimumA1()

std::string getMinimumA1

(

)

const

Returns the value of the minimum_a1 attribute.

See Hsu, J. L., et al.: "Beyond quantitative proteomics: Signal enhancement of the a(1) ion as a mass tag for peptide sequencing using dimethyl labeling". Journal of Proteome Research 4 101-108 (2005).

Returns

current value of the minimum_a1 attribute.

getMinimumA1SchemaType()

std::string getMinimumA1SchemaType

(

)

const

Obtain a symbolic name for the minimum_a1 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.

getMinPrecursorCharge()

int getMinPrecursorCharge

(

)

const

Returns the value of the min_precursor_charge attribute.

Unsigned integer, corresponding to abs(charge), in case anyone is using negative ions.

Returns

current value of the min_precursor_charge attribute.

getMinPrecursorChargeSchemaType()

std::string getMinPrecursorChargeSchemaType

(

)

const

Obtain a symbolic name for the min_precursor_charge 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.

getNumberOfParameters()

int getNumberOfParameters ( ) const

virtualinherited

Returns the number of parameters held.

Returns

total number of parameters in the list.

Implements ms_xml_parameters.

getParameterByName()

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.

getParameterByNumber()

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.

getParameterSchemaType()

std::string getParameterSchemaType ( ) const

virtualinherited

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.

getPepThresholdType()

std::string getPepThresholdType

(

)

const

Returns the value of the pep_threshold_type attribute.

Type of significance threshold for peptide matches.

Returns

current value of the pep_threshold_type attribute.

getPepThresholdTypeSchemaType()

std::string getPepThresholdTypeSchemaType

(

)

const

Obtain a symbolic name for the pep_threshold_type 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.

getPepThresholdValue()

std::string getPepThresholdValue

(

)

const

Returns the value of the pep_threshold_value attribute.

Value of significance threshold for peptide matches (only used by certain threshold types).

Returns

current value of the pep_threshold_value attribute.

getPepThresholdValueSchemaType()

std::string getPepThresholdValueSchemaType

(

)

const

Obtain a symbolic name for the "pep_threshold_value" 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").

Reimplemented from ms_quant_parameters.

getTotalIntensitySchemaType()

std::string getTotalIntensitySchemaType

(

)

const

Obtain a symbolic name for the total_intensity 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.

getTotalIntensityThreshold()

std::string getTotalIntensityThreshold

(

)

const

Returns the value of the total_intensity_threshold attribute.

If TRUE, only report ratios for peptide sequences where the the totalIntensity of fitted peaks across the XIC peak exceeds the value of the total_intensity_threshold attribute.

Returns

current value of the total_intensity_threshold attribute.

getTotalIntensityThresholdSchemaType()

std::string getTotalIntensityThresholdSchemaType

(

)

const

Obtain a symbolic name for the total_intensity_threshold 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.

getUniquePepseqSchemaType()

std::string getUniquePepseqSchemaType

(

)

const

Obtain a symbolic name for the unique_pepseq 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.

haveIsolatedPrecursor()

bool haveIsolatedPrecursor

(

)

const

Indicates presence of the isolated_precursor 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.

haveIsolatedPrecursorThreshold()

bool haveIsolatedPrecursorThreshold

(

)

const

Indicates presence of the isolated_precursor_threshold 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.

haveMinimumA1()

bool haveMinimumA1

(

)

const

Indicates presence of the minimum_a1 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.

haveMinPrecursorCharge()

bool haveMinPrecursorCharge

(

)

const

Indicates presence of the min_precursor_charge 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.

havePepThresholdType()

bool havePepThresholdType

(

)

const

Indicates presence of the pep_threshold_type 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.

havePepThresholdValue()

bool havePepThresholdValue

(

)

const

Indicates presence of the pep_threshold_value 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.

haveTotalIntensity()

bool haveTotalIntensity

(

)

const

Indicates presence of the total_intensity 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.

haveTotalIntensityThreshold()

bool haveTotalIntensityThreshold

(

)

const

Indicates presence of the total_intensity_threshold 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.

haveUniquePepseq()

bool haveUniquePepseq

(

)

const

Indicates presence of the unique_pepseq 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.

isIsolatedPrecursor()

bool isIsolatedPrecursor

(

)

const

Returns the value of the isolated_precursor attribute.

Determines whether to perform test for matched_fraction.

Returns

current value of the isolated_precursor attribute.

isTotalIntensity()

bool isTotalIntensity

(

)

const

Returns the value of the total_intensity attribute.

Determines whether to apply the test for totalIntensity

Returns

current value of the total_intensity attribute.

isUniquePepseq()

bool isUniquePepseq

(

)

const

Returns the value of the unique_pepseq attribute.

If TRUE, only report ratios for peptide sequences that are unique to one protein hit (which may be a family containing multiple proteins).

Returns

current value of the unique_pepseq attribute.

operator=()

ms_quant_quality & operator=

(

const ms_quant_quality &

right

)

C++ style assignment operator.

Parameters

right

another instance of this class to copy the content from.

Returns

reference to the current object

setIsolatedPrecursor()

void setIsolatedPrecursor

(

const bool

value

)

Set a custom value for the isolated_precursor attribute.

Parameters

value

a new value for the attribute.

setIsolatedPrecursorThreshold()

void setIsolatedPrecursorThreshold

(

const char *

value

)

Set a custom value for the isolated_precursor_threshold attribute.

Parameters

value

a new value for the attribute.

setMinimumA1()

void setMinimumA1

(

const char *

value

)

Set a custom value for the minimum_a1 attribute.

Parameters

value

a new value for the attribute.

setMinPrecursorCharge()

void setMinPrecursorCharge

(

const int

value

)

Set a custom value for the min_precursor_charge attribute.

Parameters

value

a new value for the attribute.

setPepThresholdType()

void setPepThresholdType

(

const char *

value

)

Set a custom value for the pep_threshold_type attribute.

Parameters

value

a new value for the attribute.

setPepThresholdValue()

void setPepThresholdValue

(

const char *

value

)

Set a custom value for the pep_threshold_value attribute.

Parameters

value

a new value for the attribute.

setTotalIntensity()

void setTotalIntensity

(

bool

value

)

Set a custom value for the total_intensity attribute.

Parameters

value

a new value for the attribute.

setTotalIntensityThreshold()

void setTotalIntensityThreshold

(

std::string

value

)

Set a custom value for the total_intensity_threshold attribute.

Parameters

value

a new value for the attribute.

setUniquePepseq()

void setUniquePepseq

(

bool

value

)

Set a custom value for the unique_pepseq attribute.

Parameters

value

a new value for the attribute.

updateParameterByName()

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.

updateParameterByNumber()

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.

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.

---

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

• ms_quant_quality.hpp
• ms_quant_quality.cpp