ms_quant_multiplex Class Reference

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

#include <ms_quant_multiplex.hpp>

Inheritance diagram for ms_quant_multiplex:

Collaboration diagram for ms_quant_multiplex:

Public Member Functions
	ms_quant_multiplex ()
	Default constructor.
	ms_quant_multiplex (const ms_quant_multiplex &src)
	Copying constructor.
virtual	~ms_quant_multiplex ()
	Destructor.
void	appendIonSeries (const std::string ionSeries)
	Adds a new ion_series element at the end of the list.
void	appendParameter (const ms_quant_parameter *item)
	Adds a new parameter at the end of the list.
void	clearIonSeries ()
	Deletes all ions_series elements from the list.
virtual void	clearParameters ()
	Deletes all parameters from the list.
void	copyFrom (const ms_quant_multiplex *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.
bool	deleteIonSeries (const int idx)
	Remove an ion_series element from the list in memory by its index.
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	dropExcludeInternalLabel ()
	Delete the exclude_internal_label attribute.
void	dropExcludeIsobaricFragments ()
	Delete the exclude_isobaric_fragments attribute.
void	dropIonIntensityThreshold ()
	Delete the ion_intensity_threshold attribute.
void	dropIonSeries ()
	Delete the ion_series element.
void	dropMinIonPairs ()
	Delete the min_ion_pairs attribute.
std::string	getExcludeInternalLabelSchemaType () const
	Obtain a symbolic name for the exclude_internal_label element schema type.
std::string	getExcludeIsobaricFragmentsSchemaType () const
	Obtain a symbolic name for the exclude_isobaric_fragments attribute schema type.
std::string	getIonIntensityThreshold () const
	Returns the value of the ion_intensity_threshold attribute.
std::string	getIonIntensityThresholdSchemaType () const
	Obtain a symbolic name for the ion_intensity_threshold attribute schema type.
const std::string	getIonSeries (const int idx=0) const
	Returns a ion_series element object by its number.
std::string	getIonSeriesSchemaType () const
	Obtain a symbolic name for the ion_series element schema type.
int	getMinIonPairs () const
	Returns the value of the min_ion_pairs attribute.
std::string	getMinIonPairsSchemaType () const
	Obtain a symbolic name for the min_ion_pairs attribute schema type.
int	getNumberOfIonSeries () const
	Returns the number of ions series.
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	haveExcludeInternalLabel () const
	Indicates presence of the exclude_internal_label attribute.
bool	haveExcludeIsobaricFragments () const
	Indicates presence of the exclude_isobaric_fragments attribute.
bool	haveIonIntensityThreshold () const
	Indicates presence of the ion_intensity_threshold attribute.
bool	haveIonSeries () const
	Check for presence of the ion_series element.
bool	haveMinIonPairs () const
	Indicates presence of the min_ion_pairs attribute.
bool	isExcludeInternalLabel () const
	Returns the value of the exclude_internal_label attribute value.
bool	isExcludeIsobaricFragments () const
	Returns the value of the exclude_isobaric_fragments attribute.
ms_quant_multiplex &	operator= (const ms_quant_multiplex &right)
	C++ style assignment operator.
void	setExcludeInternalLabel (const bool value)
	Set a custom value for the exclude_internal_label attribute.
void	setExcludeIsobaricFragments (const bool value)
	Set a custom value for the exclude_isobaric_fragments attribute.
void	setIonIntensityThreshold (const char *value)
	Set a custom value for the ion_intensity_threshold attribute.
void	setIonSeries (const std::string ionSeries)
	Supply custom content for the ion_series element.
void	setMinIonPairs (const int value)
	Set a custom value for the min_ion_pairs attribute.
bool	updateIonSeries (const int idx, const std::string ionSeries)
	Update the information for a specific ion_series element refering to it by its index.
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 multiplex element in quantitation.xml.

Use intensities of sequence ion fragment peaks within an MS/MS spectrum.

Constructor & Destructor Documentation

ms_quant_multiplex() [1/2]

ms_quant_multiplex

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_multiplex() [2/2]

ms_quant_multiplex

(

const ms_quant_multiplex &

src

)

Copying constructor.

Parameters

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

Member Function Documentation

appendIonSeries()

void appendIonSeries

(

const std::string

ionSeries

)

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

In quantitation_1, only a single ions series was allowed for multiplex. This function supersedes setIonSeries().

Parameters

ionSeries

is the value to append.

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.

clearIonSeries()

void clearIonSeries

(

)

Deletes all ions_series elements from the list.

In quantitation_1, only a single ions series was allowed for multiplex. This function supersedes dropIonSeries().

copyFrom() [1/2]

void copyFrom

(

const ms_quant_multiplex *

right

)

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_parameters *  right )

inherited

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.

deleteIonSeries()

bool deleteIonSeries

(

const int

idx

)

Remove an ion_series element from the list in memory by its index.

Parameters

idx	should be in the range 0..getNumberOfIonSeries()-1.

Returns

true if idx is in the correct range.

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.

dropExcludeInternalLabel()

void dropExcludeInternalLabel

(

)

Delete the exclude_internal_label attribute.

Disables the attribute until it is re-set.

dropExcludeIsobaricFragments()

void dropExcludeIsobaricFragments

(

)

Delete the exclude_isobaric_fragments attribute.

Disables the attribute until it is re-set.

dropIonIntensityThreshold()

void dropIonIntensityThreshold

(

)

Delete the ion_intensity_threshold attribute.

Disables the attribute until it is re-set.

dropIonSeries()

void dropIonSeries

(

)

Delete the ion_series element.

Deprecated:

Replaced with clearIonSeries().

In quantitation_1, only a single ions series was allowed for multiplex. This function has the same effect as calling clearIonSeries().

dropMinIonPairs()

void dropMinIonPairs

(

)

Delete the min_ion_pairs attribute.

Disables the attribute until it is re-set.

getExcludeInternalLabelSchemaType()

std::string getExcludeInternalLabelSchemaType

(

)

const

Obtain a symbolic name for the exclude_internal_label 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.

getExcludeIsobaricFragmentsSchemaType()

std::string getExcludeIsobaricFragmentsSchemaType

(

)

const

Obtain a symbolic name for the exclude_isobaric_fragments 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.

getIonIntensityThreshold()

std::string getIonIntensityThreshold

(

)

const

Returns the value of the ion_intensity_threshold attribute.

Specifies fragment ion intensity threshold as fraction of base peak.

Returns

current value of the ion_intensity_threshold attribute.

getIonIntensityThresholdSchemaType()

std::string getIonIntensityThresholdSchemaType

(

)

const

Obtain a symbolic name for the ion_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.

getIonSeries()

const std::string getIonSeries

(

const int

idx = 0

)

const

Returns a ion_series element object by its number.

In quantitation_1, only a single ions series was permitted. This function returns the first ions series if no index is specified.

Parameters

idx	should be in the range 0..getNumberOfIonSeries()-1.

Returns

current element content.

getIonSeriesSchemaType()

std::string getIonSeriesSchemaType

(

)

const

Obtain a symbolic name for the ion_series 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.

getMinIonPairs()

int getMinIonPairs

(

)

const

Returns the value of the min_ion_pairs attribute.

Specifies whether to exclude fragment ions which have a potential isobaric interferences.

Returns

current value of the min_ion_pairs attribute.

getMinIonPairsSchemaType()

std::string getMinIonPairsSchemaType

(

)

const

Obtain a symbolic name for the min_ion_pairs 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.

getNumberOfIonSeries()

int getNumberOfIonSeries

(

)

const

Returns the number of ions series.

In quantitation_1, only a single ions series was allowed for multiplex.

Returns

the number of ions series specified.

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.

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.

haveExcludeInternalLabel()

bool haveExcludeInternalLabel

(

)

const

Indicates presence of the exclude_internal_label 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.

haveExcludeIsobaricFragments()

bool haveExcludeIsobaricFragments

(

)

const

Indicates presence of the exclude_isobaric_fragments 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.

haveIonIntensityThreshold()

bool haveIonIntensityThreshold

(

)

const

Indicates presence of the ion_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.

haveIonSeries()

bool haveIonSeries

(

)

const

Check for presence of the ion_series element.

In quantitation_1, only a single ions series was allowed for multiplex.

Returns

TRUE if one or more ion series are specified.

haveMinIonPairs()

bool haveMinIonPairs

(

)

const

Indicates presence of the min_ion_pairs 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.

isExcludeInternalLabel()

bool isExcludeInternalLabel

(

)

const

Returns the value of the exclude_internal_label attribute value.

TRUE value means label is allowed at terminus only.

Returns

current value of the exclude_internal_label attribute.

isExcludeIsobaricFragments()

bool isExcludeIsobaricFragments

(

)

const

Returns the value of the exclude_isobaric_fragments attribute.

Specifies whether to exclude fragment ions which have a potential isobaric interferences.

Returns

current value of the exclude_isobaric_fragments attribute.

operator=()

ms_quant_multiplex & operator=

(

const ms_quant_multiplex &

right

)

C++ style assignment operator.

Parameters

right

another instance of this class to copy the content from.

Returns

reference to the current object

setExcludeInternalLabel()

void setExcludeInternalLabel

(

const bool

value

)

Set a custom value for the exclude_internal_label attribute.

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

Parameters

value

a new value for the attribute.

setExcludeIsobaricFragments()

void setExcludeIsobaricFragments

(

const bool

value

)

Set a custom value for the exclude_isobaric_fragments attribute.

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

Parameters

value

a new value for the attribute.

setIonIntensityThreshold()

void setIonIntensityThreshold

(

const char *

value

)

Set a custom value for the ion_intensity_threshold attribute.

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

Parameters

value

a new value for the attribute.

setIonSeries()

void setIonSeries

(

const std::string

ionSeries

)

Supply custom content for the ion_series element.

Deprecated:

Replaced with appendIonSeries().

In quantitation_1, only a single ions series was allowed for multiplex. This function now clears the list of ions series and replaces the list with a single new value.

Parameters

ionSeries

a new content for the element.

setMinIonPairs()

void setMinIonPairs

(

const int

value

)

Set a custom value for the min_ion_pairs attribute.

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

Parameters

value

a new value for the attribute.

updateIonSeries()

bool updateIonSeries	(	const int	idx,
		const std::string	ionSeries
	)

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

Parameters

idx	should be in the range 0..getNumberOfIonSeries()-1.
ionSeries	is the new ions series value.

Returns

true if idx is in the correct range.

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_multiplex.hpp
• ms_quant_multiplex.cpp