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Public Member Functions

ms_quant_multiplex Class Reference
[Mascot configuration files module]

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

#include <ms_quant_multiplex.hpp>

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List of all members.

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.
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.
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 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.
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.
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_multiplexoperator= (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

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 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:
ionSeriesis the value to append.
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 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().

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 copyFrom ( const ms_quant_multiplex right )

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 deleteIonSeries ( const int  idx )

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

Parameters:
idxshould be in the range 0..getNumberOfIonSeries()-1.
Returns:
true if idx is in the correct range.
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 dropExcludeInternalLabel (  )

Delete the exclude_internal_label attribute.

Disables the attribute until it is re-set.

void dropExcludeIsobaricFragments (  )

Delete the exclude_isobaric_fragments attribute.

Disables the attribute until it is re-set.

void dropIonIntensityThreshold (  )

Delete the ion_intensity_threshold attribute.

Disables the attribute until it is re-set.

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().

void dropMinIonPairs (  )

Delete the min_ion_pairs attribute.

Disables the attribute until it is re-set.

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.
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.
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.
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.
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:
idxshould be in the range 0..getNumberOfIonSeries()-1.
Returns:
current element content.
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.
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.
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.
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.
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 getSchemaType (  ) const [virtual]

Returns name of the schema type that can be used to validate this element.

Additional information about the current object can be retrieved from the associated XML schema file. Every element in an XML document is defined with a named type, which you can use to find out what kind of limits (numerical or otherwise) are defined for values of that type.

See also:
validateShallow(), validateDeep()
Returns:
a symbolic fully qualified type name (for example, "mqm:nameType").

Reimplemented from ms_quant_parameters.

bool 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.
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.
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.
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.
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.
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.
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.
ms_quant_multiplex & operator= ( const ms_quant_multiplex right )

C++ style assignment operator.

Parameters:
rightanother instance of this class to copy the content from.
Returns:
reference to the current object
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
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:
valuea new value for the attribute.
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:
ionSeriesa new content for the element.
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:
valuea new value for the 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.

Parameters:
idxshould be in the range 0..getNumberOfIonSeries()-1.
ionSeriesis the new ions series value.
Returns:
true if idx is in the correct range.
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