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Public Member Functions

ms_quant_quality Class Reference
[Mascot configuration files module]

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

#include <ms_quant_quality.hpp>

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List of all members.

Public Member Functions

 ms_quant_quality ()
 Default constructor.
 ms_quant_quality (const ms_quant_quality &src)
 Copying constructor.
virtual ~ms_quant_quality ()
 Destructor.
void appendParameter (const ms_quant_parameter *item)
 Adds a new parameter at the end of the list.
void clearParameters ()
 Deletes all parameters from the list.
void copyFrom (const ms_quant_quality *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 dropIsolatedPrecursor ()
 Delete the isolated_precursor attribute.
void dropIsolatedPrecursorThreshold ()
 Delete the isolated_precursor_threshold attribute.
void dropMinimumA1 ()
 Delete the minimum_a1 attribute.
void dropMinPrecursorCharge ()
 Delete the min_precursor_charge attribute.
void dropPepThresholdType ()
 Delete the pep_threshold_type attribute.
void dropPepThresholdValue ()
 Delete the pep_threshold_value attribute.
void dropUniquePepseq ()
 Delete the unique_pepseq attribute.
std::string getIsolatedPrecursorSchemaType () const
 Obtain a symbolic name for the isolated_precursor attribute schema type.
std::string getIsolatedPrecursorThreshold () const
 Returns the value of the isolated_precursor_threshold attribute.
std::string getIsolatedPrecursorThresholdSchemaType () const
 Obtain a symbolic name for the isolated_precursor_threshold attribute schema type.
std::string getMinimumA1 () const
 Returns the value of the minimum_a1 attribute.
std::string getMinimumA1SchemaType () const
 Obtain a symbolic name for the minimum_a1 attribute schema type.
int getMinPrecursorCharge () const
 Returns the value of the min_precursor_charge attribute.
std::string getMinPrecursorChargeSchemaType () const
 Obtain a symbolic name for the min_precursor_charge attribute schema type.
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 getPepThresholdType () const
 Returns the value of the pep_threshold_type attribute.
std::string getPepThresholdTypeSchemaType () const
 Obtain a symbolic name for the pep_threshold_type attribute schema type.
std::string getPepThresholdValue () const
 Returns the value of the pep_threshold_value attribute.
std::string getPepThresholdValueSchemaType () const
 Obtain a symbolic name for the "pep_threshold_value" schema type.
virtual std::string getSchemaType () const
 Returns name of the schema type that can be used to validate this element.
std::string getUniquePepseqSchemaType () const
 Obtain a symbolic name for the unique_pepseq attribute schema type.
bool haveIsolatedPrecursor () const
 Indicates presence of the isolated_precursor attribute.
bool haveIsolatedPrecursorThreshold () const
 Indicates presence of the isolated_precursor_threshold attribute.
bool haveMinimumA1 () const
 Indicates presence of the minimum_a1 attribute.
bool haveMinPrecursorCharge () const
 Indicates presence of the min_precursor_charge attribute.
bool havePepThresholdType () const
 Indicates presence of the pep_threshold_type attribute.
bool havePepThresholdValue () const
 Indicates presence of the pep_threshold_value attribute.
bool haveUniquePepseq () const
 Indicates presence of the unique_pepseq attribute.
bool isIsolatedPrecursor () const
 Returns the value of the isolated_precursor attribute.
bool isUniquePepseq () const
 Returns the value of the unique_pepseq attribute.
ms_quant_qualityoperator= (const ms_quant_quality &right)
 C++ style assignment operator.
void setIsolatedPrecursor (const bool value)
 Set a custom value for the isolated_precursor attribute.
void setIsolatedPrecursorThreshold (const char *value)
 Set a custom value for the isolated_precursor_threshold attribute.
void setMinimumA1 (const char *value)
 Set a custom value for the minimum_a1 attribute.
void setMinPrecursorCharge (const int value)
 Set a custom value for the min_precursor_charge attribute.
void setPepThresholdType (const char *value)
 Set a custom value for the pep_threshold_type attribute.
void setPepThresholdValue (const char *value)
 Set a custom value for the pep_threshold_value attribute.
void setUniquePepseq (bool value)
 Set a custom value for the unique_pepseq attribute.
bool updateParameterByName (const char *name, const ms_quant_parameter *param)
 Update the information for a specific parameter refering to it by its unique name.
bool updateParameterByNumber (const int idx, const ms_quant_parameter *param)
 Update the information for a specific parameter refering to it by its index.
virtual std::string validateDeep (const ms_xml_schema *pSchemaFileObj) const
 Performs validation of all child elements in addition to 'shallow' validation.
virtual std::string validateShallow (const ms_xml_schema *pSchemaFileObj) const
 Performs simple validation of the top-level elements only.

Detailed Description

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


Constructor & Destructor Documentation

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_quality ( const ms_quant_quality src )

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_quality 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 dropIsolatedPrecursor (  )

Delete the isolated_precursor attribute.

Disables the attribute until it is re-set.

void dropIsolatedPrecursorThreshold (  )

Delete the isolated_precursor_threshold attribute.

Disables the attribute until it is re-set.

void dropMinimumA1 (  )

Delete the minimum_a1 attribute.

Disables the attribute until it is re-set.

void dropMinPrecursorCharge (  )

Delete the min_precursor_charge attribute.

Disables the attribute until it is re-set.

void dropPepThresholdType (  )

Delete the pep_threshold_type attribute.

Disables the attribute until it is re-set.

void dropPepThresholdValue (  )

Delete the pep_threshold_value attribute.

Disables the attribute until it is re-set.

void dropUniquePepseq (  )

Delete the unique_pepseq attribute.

Disables the attribute until it is re-set.

std::string getIsolatedPrecursorSchemaType (  ) const

Obtain a symbolic name for the isolated_precursor attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns:
symbolic type name for the element.
std::string getIsolatedPrecursorThreshold (  ) const

Returns the value of the isolated_precursor_threshold attribute.

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

Returns:
current value of the isolated_precursor_threshold attribute.
std::string getIsolatedPrecursorThresholdSchemaType (  ) const

Obtain a symbolic name for the isolated_precursor_threshold attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns:
symbolic type name for the element.
std::string getMinimumA1 (  ) const

Returns the value of the minimum_a1 attribute.

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

Returns:
current value of the minimum_a1 attribute.
std::string getMinimumA1SchemaType (  ) const

Obtain a symbolic name for the minimum_a1 attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns:
symbolic type name for the element.
int getMinPrecursorCharge (  ) const

Returns the value of the min_precursor_charge attribute.

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

Returns:
current value of the min_precursor_charge attribute.
std::string getMinPrecursorChargeSchemaType (  ) const

Obtain a symbolic name for the min_precursor_charge attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns:
symbolic type name for the element.
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 getPepThresholdType (  ) const

Returns the value of the pep_threshold_type attribute.

Type of significance threshold for peptide matches.

Returns:
current value of the pep_threshold_type attribute.
std::string getPepThresholdTypeSchemaType (  ) const

Obtain a symbolic name for the pep_threshold_type attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns:
symbolic type name for the element.
std::string getPepThresholdValue (  ) const

Returns the value of the pep_threshold_value attribute.

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

Returns:
current value of the pep_threshold_value attribute.
std::string getPepThresholdValueSchemaType (  ) const

Obtain a symbolic name for the "pep_threshold_value" schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns:
symbolic type name for the element.
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 getUniquePepseqSchemaType (  ) const

Obtain a symbolic name for the unique_pepseq attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns:
symbolic type name for the element.
bool haveIsolatedPrecursor (  ) const

Indicates presence of the isolated_precursor attribute.

You should always check for the presence of an attribute before retrieving its actual value.

Returns:
TRUE if the attribute is present in current element and FALSE otherwise.
bool haveIsolatedPrecursorThreshold (  ) const

Indicates presence of the isolated_precursor_threshold attribute.

You should always check for the presence of an attribute before retrieving its actual value.

Returns:
TRUE if the attribute is present in current element and FALSE otherwise.
bool haveMinimumA1 (  ) const

Indicates presence of the minimum_a1 attribute.

You should always check for the presence of an attribute before retrieving its actual value.

Returns:
TRUE if the attribute is present in current element and FALSE otherwise.
bool haveMinPrecursorCharge (  ) const

Indicates presence of the min_precursor_charge attribute.

You should always check for the presence of an attribute before retrieving its actual value.

Returns:
TRUE if the attribute is present in current element and FALSE otherwise.
bool havePepThresholdType (  ) const

Indicates presence of the pep_threshold_type attribute.

You should always check for the presence of an attribute before retrieving its actual value.

Returns:
TRUE if the attribute is present in current element and FALSE otherwise.
bool havePepThresholdValue (  ) const

Indicates presence of the pep_threshold_value attribute.

You should always check for the presence of an attribute before retrieving its actual value.

Returns:
TRUE if the attribute is present in current element and FALSE otherwise.
bool haveUniquePepseq (  ) const

Indicates presence of the unique_pepseq attribute.

You should always check for the presence of an attribute before retrieving its actual value.

Returns:
TRUE if the attribute is present in current element and FALSE otherwise.
bool isIsolatedPrecursor (  ) const

Returns the value of the isolated_precursor attribute.

Determines whether to perform test for matched_fraction.

Returns:
current value of the isolated_precursor attribute.
bool isUniquePepseq (  ) const

Returns the value of the unique_pepseq attribute.

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

Returns:
current value of the unique_pepseq attribute.
ms_quant_quality & operator= ( const ms_quant_quality right )

C++ style assignment operator.

Parameters:
rightanother instance of this class to copy the content from.
Returns:
reference to the current object
void setIsolatedPrecursor ( const bool  value )

Set a custom value for the isolated_precursor attribute.

Parameters:
valuea new value for the attribute.
void setIsolatedPrecursorThreshold ( const char *  value )

Set a custom value for the isolated_precursor_threshold attribute.

Parameters:
valuea new value for the attribute.
void setMinimumA1 ( const char *  value )

Set a custom value for the minimum_a1 attribute.

Parameters:
valuea new value for the attribute.
void setMinPrecursorCharge ( const int  value )

Set a custom value for the min_precursor_charge attribute.

Parameters:
valuea new value for the attribute.
void setPepThresholdType ( const char *  value )

Set a custom value for the pep_threshold_type attribute.

Parameters:
valuea new value for the attribute.
void setPepThresholdValue ( const char *  value )

Set a custom value for the pep_threshold_value attribute.

Parameters:
valuea new value for the attribute.
void setUniquePepseq ( bool  value )

Set a custom value for the unique_pepseq attribute.

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