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

#include <ms_quant_integration.hpp>

Inheritance diagram for ms_quant_integration:

Collaboration diagram for ms_quant_integration:

Public Member Functions
	ms_quant_integration ()
	Default constructor.

	ms_quant_integration (const ms_quant_integration &src)
	Copying constructor.

virtual	~ms_quant_integration ()
	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_integration *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 ()
	Delete the `all_charge_states` attribute.

void	dropAllChargeStatesThreshold ()
	Delete the `all_charge_states_threshold` attribute.

void	dropAllowElutionShift ()
	Delete the `allow_elution_shift` attribute.

void	dropElutionProfileCorrelationThreshold ()
	Delete the `elution_profile_correlation_threshold` attribute.

void	dropElutionTimeDelta ()
	Delete the `elution_time_delta` attribute.

void	dropElutionTimeDeltaUnit ()
	Delete the `elution_time_delta_unit` attribute.

void	dropMassDelta ()

void	dropMassDeltaUnit ()

void	dropMatchedRho ()
	Delete the `matched_rho` attribute.

void	dropMethod ()
	Delete the `method` attribute.

void	dropPrecursorRange ()

void	dropProcessingOptions ()

void	dropSimpleRatio ()
	Delete the `simple_ratio` attribute.

void	dropSource ()
	Delete the `source` attribute.

void	dropXicMaxWidth ()
	Delete the `xic_max_width` attribute.

void	dropXicSmoothing ()
	Delete the `xic_smoothing` attribute.

void	dropXicThreshold ()
	Delete the `xic_threshold` attribute.

std::string	getAllChargeStatesSchemaType () const
	Obtain a symbolic name for the `all_charge_states` attribute schema type.

std::string	getAllChargeStatesThreshold () const
	Returns the value of the `all_charge_states_threshold` attribute.

std::string	getAllChargeStatesThresholdSchemaType () const
	Obtain a symbolic name for the `all_charge_states_threshold` attribute schema type.

std::string	getAllowElutionShiftSchemaType () const
	Obtain a symbolic name for the `allow_elution_shift` attribute schema type.

std::string	getElutionProfileCorrelationThreshold () const
	Returns the value of the `elution_profile_correlation_threshold` attribute.

std::string	getElutionProfileCorrelationThresholdSchemaType () const
	Obtain a symbolic name for the `elution_profile_correlation_threshold` attribute schema type.

std::string	getElutionTimeDelta () const
	Returns the value of the `elution_time_delta` attribute.

std::string	getElutionTimeDeltaSchemaType () const
	Obtain a symbolic name for the `elution_time_delta` attribute schema type.

std::string	getElutionTimeDeltaUnit () const
	Returns the value of the `elution_time_delta_unit` attribute.

std::string	getElutionTimeDeltaUnitSchemaType () const
	Obtain a symbolic name for the `elution_time_delta_unit` attribute schema type.

std::string	getMassDelta () const

std::string	getMassDeltaSchemaType () const

std::string	getMassDeltaUnit () const

std::string	getMassDeltaUnitSchemaType () const

std::string	getMatchedRho () const
	Returns the value of the `matched_rho` attribute.

std::string	getMatchedRhoSchemaType () const
	Obtain a symbolic name for the `matched_rho` attribute schema type.

std::string	getMethod () const
	Returns the value of the `method` attribute.

std::string	getMethodSchemaType () const
	Obtain a symbolic name for the `method` 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	getPrecursorRange () const

std::string	getPrecursorRangeSchemaType () const

std::string	getProcessingOptions () const

std::string	getProcessingOptionsSchemaType () const

virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.

std::string	getSimpleRatioSchemaType () const
	Obtain a symbolic name for the `simple_ratio` attribute schema type.

std::string	getSource () const
	Returns the value of the `source` attribute.

std::string	getSourceSchemaType () const
	Obtain a symbolic name for the `source` attribute schema type.

int	getXicMaxWidth () const
	Returns the value of the `xic_max_width` attribute.

std::string	getXicMaxWidthSchemaType () const
	Obtain a symbolic name for the "xic_max_width" schema type.

int	getXicSmoothing () const
	Returns the value of the `xic_smoothing` attribute.

std::string	getXicSmoothingSchemaType () const
	Obtain a symbolic name for the `xic_smoothing` attribute schema type.

std::string	getXicThreshold () const
	Returns the value of the `xic_threshold` attribute.

std::string	getXicThresholdSchemaType () const
	Obtain a symbolic name for the `xic_threshold` attribute schema type.

bool	haveAllChargeStates () const
	Indicates presence of the `all_charge_states` attribute.

bool	haveAllChargeStatesThreshold () const
	Indicates presence of the `all_charge_states_threshold` attribute.

bool	haveAllowElutionShift () const
	Indicates presence of the `allow_elution_shift` attribute.

bool	haveElutionProfileCorrelationThreshold () const
	Indicates presence of the `elution_profile_correlation_threshold` attribute.

bool	haveElutionTimeDelta () const
	Indicates presence of the `elution_time_delta` attribute.

bool	haveElutionTimeDeltaUnit () const
	Indicates presence of the `elution_time_delta_unit` attribute.

bool	haveMassDelta () const

bool	haveMassDeltaUnit () const

bool	haveMatchedRho () const
	Indicates presence of the `matched_rho` attribute.

bool	haveMethod () const
	Indicates presence of the `method` attribute.

bool	havePrecursorRange () const

bool	haveProcessingOptions () const

bool	haveSimpleRatio () const
	Indicates presence of the `simple_ratio` attribute.

bool	haveSource () const
	Indicates presence of the `source` attribute.

bool	haveXicMaxWidth () const
	Indicates presence of the `xic_max_width` attribute.

bool	haveXicSmoothing () const
	Indicates presence of the `xic_smoothing` attribute.

bool	haveXicThreshold () const
	Indicates presence of the `xic_threshold` attribute.

bool	isAllChargeStates () const
	Returns the value of the `all_charge_states` attribute.

bool	isAllowElutionShift () const
	Returns the value of the `allow_elution_shift` attribute.

bool	isSimpleRatio () const
	Returns the value of the `simple_ratio` attribute.

ms_quant_integration &	operator= (const ms_quant_integration &right)
	C++ style assignment operator.

void	setAllChargeStates (const bool value)
	Set a custom value for the `all_charge_states` attribute.

void	setAllChargeStatesThreshold (const char *value)
	Set a custom value for the `all_charge_states_threshold` attribute.

void	setAllowElutionShift (const bool value)
	Set a custom value for the `allow_elution_shift` attribute.

void	setElutionProfileCorrelationThreshold (const char *value)
	Set a custom value for the `elution_profile_correlation_threshold` attribute.

void	setElutionTimeDelta (const char *value)
	Set a custom value for the `elution_time_delta` attribute.

void	setElutionTimeDeltaUnit (const char *value)
	Set a custom value for the `elution_time_delta_unit` attribute.

void	setMassDelta (const char *value)

void	setMassDeltaUnit (const char *value)

void	setMatchedRho (const char *value)
	Set a custom value for the `matched_rho` attribute.

void	setMethod (const char *value)
	Set a custom value for the `method` attribute.

void	setPrecursorRange (const char *value)

void	setProcessingOptions (const std::string value)

void	setSimpleRatio (const bool value)
	Set a custom value for the `simple_ratio` attribute.

void	setSource (const char *value)
	Set a custom value for the `source` attribute.

void	setXicMaxWidth (int value)
	Set a custom value for the `xic_max_width` attribute.

void	setXicSmoothing (int value)
	Set a custom value for the `xic_smoothing` attribute.

void	setXicThreshold (const char *value)
	Set a custom value for the `xic_threshold` 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 integration element in quantitation.xml.

Specifies the method and parameters to be used to integrate precursor over time.

Constructor & Destructor Documentation

◆ ms_quant_integration() [1/2]

ms_quant_integration ( )

Default constructor.

Assigns reasonable default values to all internal members.

◆ ms_quant_integration() [2/2]

ms_quant_integration ( const ms_quant_integration & 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_integration * 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.

◆ 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.

◆ dropAllChargeStates()

void dropAllChargeStates ( )

Delete the all_charge_states attribute.

Disables the attribute until it is re-set.

◆ dropAllChargeStatesThreshold()

void dropAllChargeStatesThreshold ( )

Delete the all_charge_states_threshold attribute.

Disables the attribute until it is re-set.

◆ dropAllowElutionShift()

void dropAllowElutionShift ( )

Delete the allow_elution_shift attribute.

Disables the attribute until it is re-set.

◆ dropElutionProfileCorrelationThreshold()

void dropElutionProfileCorrelationThreshold ( )

Delete the elution_profile_correlation_threshold attribute.

Disables the attribute until it is re-set.

◆ dropElutionTimeDelta()

void dropElutionTimeDelta ( )

Delete the elution_time_delta attribute.

Disables the attribute until it is re-set.

◆ dropElutionTimeDeltaUnit()

void dropElutionTimeDeltaUnit ( )

Delete the elution_time_delta_unit attribute.

Disables the attribute until it is re-set.

◆ dropMassDelta()

void dropMassDelta ( )

Deprecated:: Not in use.

◆ dropMassDeltaUnit()

void dropMassDeltaUnit ( )

Deprecated:: Not in use.

◆ dropMatchedRho()

void dropMatchedRho ( )

Delete the matched_rho attribute.

Disables the attribute until it is re-set.

◆ dropMethod()

void dropMethod ( )

Delete the method attribute.

Disables the attribute until it is re-set.

◆ dropPrecursorRange()

void dropPrecursorRange ( )

Deprecated:: Do not use.

◆ dropProcessingOptions()

void dropProcessingOptions ( )

Deprecated:: Do not use.

◆ dropSimpleRatio()

void dropSimpleRatio ( )

Delete the simple_ratio attribute.

Disables the attribute until it is re-set.

◆ dropSource()

void dropSource ( )

Delete the source attribute.

Disables the attribute until it is re-set.

◆ dropXicMaxWidth()

void dropXicMaxWidth ( )

Delete the xic_max_width attribute.

Disables the attribute until it is re-set.

◆ dropXicSmoothing()

void dropXicSmoothing ( )

Delete the xic_smoothing attribute.

Disables the attribute until it is re-set.

◆ dropXicThreshold()

void dropXicThreshold ( )

Delete the xic_threshold attribute.

Disables the attribute until it is re-set.

◆ getAllChargeStatesSchemaType()

std::string getAllChargeStatesSchemaType ( ) const

Obtain a symbolic name for the all_charge_states 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.

◆ getAllChargeStatesThreshold()

std::string getAllChargeStatesThreshold ( ) const

Returns the value of the all_charge_states_threshold attribute.

When all_charge_states is true, additional contiguous charge states are included in quantitation if their intensity exceeds this fraction of the the most intense charge state for which there is a database match.

Returns: current value of the all_charge_states_threshold attribute.

◆ getAllChargeStatesThresholdSchemaType()

std::string getAllChargeStatesThresholdSchemaType ( ) const

Obtain a symbolic name for the all_charge_states_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.

◆ getAllowElutionShiftSchemaType()

std::string getAllowElutionShiftSchemaType ( ) const

Obtain a symbolic name for the allow_elution_shift 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.

◆ getElutionProfileCorrelationThreshold()

std::string getElutionProfileCorrelationThreshold ( ) const

Returns the value of the elution_profile_correlation_threshold attribute.

Threshold on the standard error for a straight line fit of the component intensities from each of the scans in the XIC peak.

Returns: current value of the elution_profile_correlation_threshold attribute.

◆ getElutionProfileCorrelationThresholdSchemaType()

std::string getElutionProfileCorrelationThresholdSchemaType ( ) const

Obtain a symbolic name for the elution_profile_correlation_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.

◆ getElutionTimeDelta()

std::string getElutionTimeDelta ( ) const

Returns the value of the elution_time_delta attribute.

Elution time difference allowed when trying to pair up components.

Returns: current value of the elution_time_delta attribute.

◆ getElutionTimeDeltaSchemaType()

std::string getElutionTimeDeltaSchemaType ( ) const

Obtain a symbolic name for the elution_time_delta 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.

◆ getElutionTimeDeltaUnit()

std::string getElutionTimeDeltaUnit ( ) const

Returns the value of the elution_time_delta_unit attribute.

Units for the elution_time_delta attribute.

Returns: current value of the elution_time_delta_unit attribute.

◆ getElutionTimeDeltaUnitSchemaType()

std::string getElutionTimeDeltaUnitSchemaType ( ) const

Obtain a symbolic name for the elution_time_delta_unit 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.

◆ getMassDelta()

std::string getMassDelta ( ) const

Deprecated:: Not in use.

Returns: mass delta

◆ getMassDeltaSchemaType()

std::string getMassDeltaSchemaType ( ) const

Deprecated:: Not in use.

Returns: mass delta schema type

◆ getMassDeltaUnit()

std::string getMassDeltaUnit ( ) const

Deprecated:: Not in use.

Returns: mass delta unit

◆ getMassDeltaUnitSchemaType()

std::string getMassDeltaUnitSchemaType ( ) const

Deprecated:: Not in use.

Returns: mass delta unit schema type

◆ getMatchedRho()

std::string getMatchedRho ( ) const

Returns the value of the matched_rho attribute.

Threshold on the correlation coefficient between the predicted and observed precursor isotope distributions.

Returns: current value of the matched_rho attribute.

◆ getMatchedRhoSchemaType()

std::string getMatchedRhoSchemaType ( ) const

Obtain a symbolic name for the matched_rho 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.

◆ getMethod()

std::string getMethod ( ) const

Returns the value of the method attribute.

The method attribute specifies an integration algorithm.

Returns: current value of the method attribute.

◆ getMethodSchemaType()

std::string getMethodSchemaType ( ) const

Obtain a symbolic name for the method 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.

◆ getPrecursorRange()

std::string getPrecursorRange ( ) const

Deprecated:: Do not use.

Returns: precursor range

◆ getPrecursorRangeSchemaType()

std::string getPrecursorRangeSchemaType ( ) const

Deprecated:: Do not use.

Returns: precursor range schema type

◆ getProcessingOptions()

std::string getProcessingOptions ( ) const

Deprecated:: Do not use.

Returns: processing options

◆ getProcessingOptionsSchemaType()

std::string getProcessingOptionsSchemaType ( ) const

Deprecated:: Do not use.

Returns: processing options schema type

◆ 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.

◆ getSimpleRatioSchemaType()

std::string getSimpleRatioSchemaType ( ) const

Obtain a symbolic name for the simple_ratio 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.

◆ getSource()

std::string getSource ( ) const

Returns the value of the source attribute.

Scan type containing data to be integrated.

Returns: current value of the source attribute.

◆ getSourceSchemaType()

std::string getSourceSchemaType ( ) const

Obtain a symbolic name for the source 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.

◆ getXicMaxWidth()

int getXicMaxWidth ( ) const

Returns the value of the xic_max_width attribute.

Upper limit on the number of survey scans in an XIC peak.

Returns: current value of the xic_max_width attribute.

◆ getXicMaxWidthSchemaType()

std::string getXicMaxWidthSchemaType ( ) const

Obtain a symbolic name for the "xic_max_width" 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.

◆ getXicSmoothing()

int getXicSmoothing ( ) const

Returns the value of the xic_smoothing attribute.

XIC peak is smoothed by a set of 2n+1 Savitzky-Golay convolution integers, where n is this value (0 corresponds to no smoothing).

Returns: current value of the xic_smoothing attribute.

◆ getXicSmoothingSchemaType()

std::string getXicSmoothingSchemaType ( ) const

Obtain a symbolic name for the xic_smoothing 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.

◆ getXicThreshold()

std::string getXicThreshold ( ) const

Returns the value of the xic_threshold attribute.

The start and end of an XIC peak are where the intensity drops to this fraction of the intensity of the XIC peak maximum.

Returns: current value of the xic_threshold attribute.

◆ getXicThresholdSchemaType()

std::string getXicThresholdSchemaType ( ) const

Obtain a symbolic name for the xic_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.

◆ haveAllChargeStates()

bool haveAllChargeStates ( ) const

Indicates presence of the all_charge_states 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.

◆ haveAllChargeStatesThreshold()

bool haveAllChargeStatesThreshold ( ) const

Indicates presence of the all_charge_states_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.

◆ haveAllowElutionShift()

bool haveAllowElutionShift ( ) const

Indicates presence of the allow_elution_shift 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.

◆ haveElutionProfileCorrelationThreshold()

bool haveElutionProfileCorrelationThreshold ( ) const

Indicates presence of the elution_profile_correlation_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.

◆ haveElutionTimeDelta()

bool haveElutionTimeDelta ( ) const

Indicates presence of the elution_time_delta 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.

◆ haveElutionTimeDeltaUnit()

bool haveElutionTimeDeltaUnit ( ) const

Indicates presence of the elution_time_delta_unit 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.

◆ haveMassDelta()

bool haveMassDelta ( ) const

Deprecated:: Not in use.

Returns: true if mass delta is set, false otherwise

◆ haveMassDeltaUnit()

bool haveMassDeltaUnit ( ) const

Deprecated:: Not in use.

Returns: true if mass delta unit is set, false otherwise

◆ haveMatchedRho()

bool haveMatchedRho ( ) const

Indicates presence of the matched_rho 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.

◆ haveMethod()

bool haveMethod ( ) const

Indicates presence of the method 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.

◆ havePrecursorRange()

bool havePrecursorRange ( ) const

Deprecated:: Do not use.

Returns: true if precusor range is set, false otherwise

◆ haveProcessingOptions()

bool haveProcessingOptions ( ) const

Deprecated:: Do not use.

Returns: true if processing options is set, false otherwise

◆ haveSimpleRatio()

bool haveSimpleRatio ( ) const

Indicates presence of the simple_ratio 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.

◆ haveSource()

bool haveSource ( ) const

Indicates presence of the source 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.

◆ haveXicMaxWidth()

bool haveXicMaxWidth ( ) const

Indicates presence of the xic_max_width 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.

◆ haveXicSmoothing()

bool haveXicSmoothing ( ) const

Indicates presence of the xic_smoothing 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.

◆ haveXicThreshold()

bool haveXicThreshold ( ) const

Indicates presence of the xic_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.

◆ isAllChargeStates()

bool isAllChargeStates ( ) const

Returns the value of the all_charge_states attribute.

All charge states extends the mass and time matching to cover contiguous charge states. In other words, if there is a positive match on 2+, the software will look for 1+ and 3+. It will not look for 4+ unless 3+ is found, etc.

Returns: current attribute value.

◆ isAllowElutionShift()

bool isAllowElutionShift ( ) const

Returns the value of the allow_elution_shift attribute.

Returns: current attribute value.

◆ isSimpleRatio()

bool isSimpleRatio ( ) const

Returns the value of the simple_ratio attribute.

Returns: current attribute value.

◆ operator=()

ms_quant_integration & operator= ( const ms_quant_integration & right )

C++ style assignment operator.

Parameters

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

Returns: reference to the current object

◆ setAllChargeStates()

void setAllChargeStates ( const bool value )

Set a custom value for the all_charge_states attribute.

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

Parameters

value a new value for the attribute.

◆ setAllChargeStatesThreshold()

void setAllChargeStatesThreshold ( const char * value )

Set a custom value for the all_charge_states_threshold attribute.

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

Parameters

value a new value for the attribute.

◆ setAllowElutionShift()

void setAllowElutionShift ( const bool value )

Set a custom value for the allow_elution_shift attribute.

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

Parameters

value a new value for the attribute.

◆ setElutionProfileCorrelationThreshold()

void setElutionProfileCorrelationThreshold ( const char * value )

Set a custom value for the elution_profile_correlation_threshold attribute.

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

Parameters

value a new value for the attribute.

◆ setElutionTimeDelta()

void setElutionTimeDelta ( const char * value )

Set a custom value for the elution_time_delta attribute.

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

Parameters

value a new value for the attribute.

◆ setElutionTimeDeltaUnit()

void setElutionTimeDeltaUnit ( const char * value )

Set a custom value for the elution_time_delta_unit attribute.

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

Parameters

value a new value for the attribute.

◆ setMassDelta()

void setMassDelta ( const char * value )

Deprecated:: Not in use.

Parameters

value mass delta

◆ setMassDeltaUnit()

void setMassDeltaUnit ( const char * value )

Deprecated:: Not in use.

Parameters

value mass delta unit

◆ setMatchedRho()

void setMatchedRho ( const char * value )

Set a custom value for the matched_rho attribute.

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

Parameters

value a new value for the attribute.

◆ setMethod()

void setMethod ( const char * value )

Set a custom value for the method attribute.

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

Parameters

value a new value for the attribute.

◆ setPrecursorRange()

void setPrecursorRange ( const char * value )

Deprecated:: Do not use.

Parameters

value precursor range

◆ setProcessingOptions()

void setProcessingOptions ( const std::string value )

Deprecated:: Do not use.

Parameters

value processing options

◆ setSimpleRatio()

void setSimpleRatio ( const bool value )

Set a custom value for the simple_ratio attribute.

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

Parameters

value a new value for the attribute.

◆ setSource()

void setSource ( const char * value )

Set a custom value for the source attribute.

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

Parameters

value a new value for the attribute.

◆ setXicMaxWidth()

void setXicMaxWidth ( int value )

Set a custom value for the xic_max_width attribute.

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

Parameters

value a new value for the attribute.

◆ setXicSmoothing()

void setXicSmoothing ( int value )

Set a custom value for the xic_smoothing attribute.

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

Parameters

value a new value for the attribute.

◆ setXicThreshold()

void setXicThreshold ( const char * value )

Set a custom value for the xic_threshold attribute.

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

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_integration.hpp
ms_quant_integration.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ms_quant_integration() [1/2]

◆ ms_quant_integration() [2/2]

Member Function Documentation

◆ appendParameter()

◆ copyFrom() [1/2]

◆ copyFrom() [2/2]

◆ defaultValues()

◆ deleteParameterByName()

◆ deleteParameterByNumber()

◆ dropAllChargeStates()

◆ dropAllChargeStatesThreshold()

◆ dropAllowElutionShift()

◆ dropElutionProfileCorrelationThreshold()

◆ dropElutionTimeDelta()

◆ dropElutionTimeDeltaUnit()

◆ dropMassDelta()

◆ dropMassDeltaUnit()

◆ dropMatchedRho()

◆ dropMethod()

◆ dropPrecursorRange()

◆ dropProcessingOptions()

◆ dropSimpleRatio()

◆ dropSource()

◆ dropXicMaxWidth()

◆ dropXicSmoothing()

◆ dropXicThreshold()

◆ getAllChargeStatesSchemaType()

◆ getAllChargeStatesThreshold()

◆ getAllChargeStatesThresholdSchemaType()

◆ getAllowElutionShiftSchemaType()

◆ getElutionProfileCorrelationThreshold()

◆ getElutionProfileCorrelationThresholdSchemaType()

◆ getElutionTimeDelta()

◆ getElutionTimeDeltaSchemaType()

◆ getElutionTimeDeltaUnit()

◆ getElutionTimeDeltaUnitSchemaType()

◆ getMassDelta()

◆ getMassDeltaSchemaType()

◆ getMassDeltaUnit()

◆ getMassDeltaUnitSchemaType()

◆ getMatchedRho()

◆ getMatchedRhoSchemaType()

◆ getMethod()

◆ getMethodSchemaType()

◆ getNumberOfParameters()

◆ getParameterByName()

◆ getParameterByNumber()

◆ getParameterSchemaType()

◆ getPrecursorRange()

◆ getPrecursorRangeSchemaType()

◆ getProcessingOptions()

◆ getProcessingOptionsSchemaType()

◆ getSchemaType()

◆ getSimpleRatioSchemaType()

◆ getSource()

◆ getSourceSchemaType()

◆ getXicMaxWidth()

◆ getXicMaxWidthSchemaType()

◆ getXicSmoothing()

◆ getXicSmoothingSchemaType()

◆ getXicThreshold()

◆ getXicThresholdSchemaType()

◆ haveAllChargeStates()

◆ haveAllChargeStatesThreshold()

◆ haveAllowElutionShift()

◆ haveElutionProfileCorrelationThreshold()

◆ haveElutionTimeDelta()

◆ haveElutionTimeDeltaUnit()

◆ haveMassDelta()

◆ haveMassDeltaUnit()

◆ haveMatchedRho()

◆ haveMethod()

◆ havePrecursorRange()

◆ haveProcessingOptions()

◆ haveSimpleRatio()

◆ haveSource()

◆ haveXicMaxWidth()