Matrix Science header
Public Member Functions

ms_quant_integration Class Reference
[Mascot configuration files module]

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

#include <ms_quant_integration.hpp>

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List of all members.

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.
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.
bool deleteParameterByName (const char *name)
 Remove a parameter from the list in memory by its unique name.
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.
int getNumberOfParameters () const
 Returns the number of parameters held.
const ms_quant_parametergetParameterByName (const char *name) const
 Returns a parameter object by its name or a null value in case of not found.
const ms_quant_parametergetParameterByNumber (const int idx) const
 Returns a parameter object by its number.
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_integrationoperator= (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

Default constructor.

Assigns reasonable default values to all internal members.

Copying constructor.

Parameters:
srcanother 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:
iteman instance of parameter object to copy content from.
void copyFrom ( const ms_quant_integration right )

Copies all content from another instance.

Parameters:
rightanother instance of this class to copy the content from.
void copyFrom ( const ms_quant_parameters right ) [inherited]

Copies all content from another instance.

Parameters:
rightanother 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 ) [inherited]

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

Parameters:
namename of the parameter for deletion.
Returns:
TRUE if the parameter has been found and successfully deleted and FALSE otherwise.
bool deleteParameterByNumber ( const int  idx ) [inherited]

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

Parameters:
idxnumber of the parameter for deletion from 0 to (getNumberOfParameters() - 1).
Returns:
TRUE if the parameter has been found and successfully deleted and FALSE otherwise.
void dropAllChargeStates (  )

Delete the all_charge_states attribute.

Disables the attribute until it is re-set.

void dropAllChargeStatesThreshold (  )

Delete the all_charge_states_threshold attribute.

Disables the attribute until it is re-set.

void dropAllowElutionShift (  )

Delete the allow_elution_shift attribute.

Disables the attribute until it is re-set.

void dropElutionProfileCorrelationThreshold (  )

Delete the elution_profile_correlation_threshold attribute.

Disables the attribute until it is re-set.

void dropElutionTimeDelta (  )

Delete the elution_time_delta attribute.

Disables the attribute until it is re-set.

void dropElutionTimeDeltaUnit (  )

Delete the elution_time_delta_unit attribute.

Disables the attribute until it is re-set.

void dropMassDelta (  )
Deprecated:
Not in use.
void dropMassDeltaUnit (  )
Deprecated:
Not in use.
void dropMatchedRho (  )

Delete the matched_rho attribute.

Disables the attribute until it is re-set.

void dropMethod (  )

Delete the method attribute.

Disables the attribute until it is re-set.

void dropPrecursorRange (  )
Deprecated:
Do not use.
void dropProcessingOptions (  )
Deprecated:
Do not use.
void dropSimpleRatio (  )

Delete the simple_ratio attribute.

Disables the attribute until it is re-set.

void dropSource (  )

Delete the source attribute.

Disables the attribute until it is re-set.

void dropXicMaxWidth (  )

Delete the xic_max_width attribute.

Disables the attribute until it is re-set.

void dropXicSmoothing (  )

Delete the xic_smoothing attribute.

Disables the attribute until it is re-set.

void dropXicThreshold (  )

Delete the xic_threshold attribute.

Disables the attribute until it is re-set.

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
std::string getMassDelta (  ) const
Deprecated:
Not in use.
Returns:
mass delta
std::string getMassDeltaSchemaType (  ) const
Deprecated:
Not in use.
Returns:
mass delta schema type
std::string getMassDeltaUnit (  ) const
Deprecated:
Not in use.
Returns:
mass delta unit
std::string getMassDeltaUnitSchemaType (  ) const
Deprecated:
Not in use.
Returns:
mass delta unit schema type
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.
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.
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.
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.
int getNumberOfParameters (  ) const [inherited]

Returns the number of parameters held.

Returns:
total number of parameters in the list.
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:
namename 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:
idxnumber 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 [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.
std::string getPrecursorRange (  ) const
Deprecated:
Do not use.
Returns:
precursor range
std::string getPrecursorRangeSchemaType (  ) const
Deprecated:
Do not use.
Returns:
precursor range schema type
std::string getProcessingOptions (  ) const
Deprecated:
Do not use.
Returns:
processing options
std::string getProcessingOptionsSchemaType (  ) const
Deprecated:
Do not use.
Returns:
processing options schema type
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.

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
bool haveMassDelta (  ) const
Deprecated:
Not in use.
Returns:
true if mass delta is set, false otherwise
bool haveMassDeltaUnit (  ) const
Deprecated:
Not in use.
Returns:
true if mass delta unit is set, false otherwise
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.
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.
bool havePrecursorRange (  ) const
Deprecated:
Do not use.
Returns:
true if precusor range is set, false otherwise
bool haveProcessingOptions (  ) const
Deprecated:
Do not use.
Returns:
true if processing options is set, false otherwise
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.
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.
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.
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.
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.
bool isAllChargeStates (  ) const

Returns the value of the all_charge_states attribute.

Returns:
current attribute value.
bool isAllowElutionShift (  ) const

Returns the value of the allow_elution_shift attribute.

Returns:
current attribute value.
bool isSimpleRatio (  ) const

Returns the value of the simple_ratio attribute.

Returns:
current attribute value.
ms_quant_integration & operator= ( const ms_quant_integration right )

C++ style assignment operator.

Parameters:
rightanother instance of this class to copy the content from.
Returns:
reference to the current object
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
void setMassDelta ( const char *  value )
Deprecated:
Not in use.
Parameters:
valuemass delta
void setMassDeltaUnit ( const char *  value )
Deprecated:
Not in use.
Parameters:
valuemass delta unit
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
void setPrecursorRange ( const char *  value )
Deprecated:
Do not use.
Parameters:
valueprecursor range
void setProcessingOptions ( const std::string  value )
Deprecated:
Do not use.
Parameters:
valueprocessing options
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
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:
valuea 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:
namename of the parameter for updating.
paraman 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:
idxnumber of the parameter for updating from 0 to (getNumberOfParameters() - 1).
paraman 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:
pSchemaFileObja 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_quant_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:
pSchemaFileObja 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_quant_parameters.


The documentation for this class was generated from the following files:
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:54