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Public Member Functions

ms_quant_average Class Reference
[Mascot configuration files module]

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

#include <ms_quant_average.hpp>

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List of all members.

Public Member Functions

 ms_quant_average ()
 Default constructor.
 ms_quant_average (const ms_quant_average &src)
 Copying constructor.
virtual ~ms_quant_average ()
 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_parameters *right)
 Copies all content from another instance.
void copyFrom (const ms_quant_average *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 dropNumPeptides ()
 Delete the num_peptides attribute.
void dropReferenceAccession ()
 Delete the reference_accession attribute.
void dropReferenceAmount ()
 Delete the reference_amount attribute.
void dropReferenceDatabase ()
 Delete the reference_database attribute.
void dropSelection ()
 Delete the selection attribute.
int getNumberOfParameters () const
 Returns the number of parameters held.
int getNumPeptides () const
 Returns the value of the num_peptides attribute.
std::string getNumPeptidesSchemaType () const
 Obtain a symbolic name for the num_peptides attribute schema type.
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 getReferenceAccession () const
 Returns the value of the reference_accession attribute.
std::string getReferenceAccessionSchemaType () const
 Obtain a symbolic name for the reference_accession attribute schema type.
std::string getReferenceAmount () const
 Returns the value of the reference_amount attribute.
std::string getReferenceAmountSchemaType () const
 Obtain a symbolic name for the reference_amount attribute schema type.
std::string getReferenceDatabase () const
 Returns the value of the reference_database attribute.
std::string getReferenceDatabaseSchemaType () const
 Obtain a symbolic name for the reference_database attribute schema type.
virtual std::string getSchemaType () const
 Returns name of the schema type that can be used to validate this element.
std::string getSelection () const
 Returns the value of the selection attribute.
std::string getSelectionSchemaType () const
 Obtain a symbolic name for the selection attribute schema type.
bool haveNumPeptides () const
 Indicates presence of the num_peptides attribute.
bool haveReferenceAccession () const
 Indicates presence of the reference_accession attribute.
bool haveReferenceAmount () const
 Indicates presence of the reference_amount attribute.
bool haveReferenceDatabase () const
 Indicates presence of the reference_database attribute.
bool haveSelection () const
 Indicates presence of the selection attribute.
ms_quant_averageoperator= (const ms_quant_average &right)
 C++ style assignment operator.
void setNumPeptides (int value)
 Set a custom value for the num_peptides attribute.
void setReferenceAccession (const char *value)
 Set a custom value for the reference_accession attribute.
void setReferenceAmount (const char *value)
 Set a custom value for the reference_amount attribute.
void setReferenceDatabase (const char *value)
 Set a custom value for the reference_database attribute.
void setSelection (const char *value)
 Set a custom value for the selection 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 "average" element in quantitation.xml.

Serves as a possible sub-element of the "protocol" element.


Constructor & Destructor Documentation

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_average ( const ms_quant_average 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_average 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 dropNumPeptides (  )

Delete the num_peptides attribute.

Disables the attribute until it is re-set.

void dropReferenceAccession (  )

Delete the reference_accession attribute.

Disables the attribute until it is re-set.

void dropReferenceAmount (  )

Delete the reference_amount attribute.

Disables the attribute until it is re-set.

void dropReferenceDatabase (  )

Delete the reference_database attribute.

Disables the attribute until it is re-set.

void dropSelection (  )

Delete the selection attribute.

Disables the attribute until it is re-set.

int getNumberOfParameters (  ) const [inherited]

Returns the number of parameters held.

Returns:
total number of parameters in the list.
int getNumPeptides (  ) const

Returns the value of the num_peptides attribute.

Number of peptides per protein to be used for quantitation.

Returns:
current value of "num_peptides" attribute.
std::string getNumPeptidesSchemaType (  ) const

Obtain a symbolic name for the num_peptides 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 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 getReferenceAccession (  ) const

Returns the value of the reference_accession attribute.

Database accession for reference protein.

Returns:
current value of the "reference_accession" attribute.
std::string getReferenceAccessionSchemaType (  ) const

Obtain a symbolic name for the reference_accession 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 getReferenceAmount (  ) const

Returns the value of the reference_amount attribute.

Amount of reference protein.

Returns:
current value of the "reference_amount" attribute.
std::string getReferenceAmountSchemaType (  ) const

Obtain a symbolic name for the reference_amount 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 getReferenceDatabase (  ) const

Returns the value of the reference_database attribute.

Database database for reference protein.

Returns:
current value of the "reference_database" attribute.
std::string getReferenceDatabaseSchemaType (  ) const

Obtain a symbolic name for the reference_database 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 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 getSelection (  ) const

Returns the value of the selection attribute.

Whether to require the peptides to be used for quantitation to be unique sequences, or to accept different modification states of same sequence (unique_mr), or even accept peptides with same sequence and modifications in different charge states (unique_mz).

Returns:
current value of the "selection" attribute.
std::string getSelectionSchemaType (  ) const

Obtain a symbolic name for the selection 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 haveNumPeptides (  ) const

Indicates presence of the num_peptides 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 haveReferenceAccession (  ) const

Indicates presence of the reference_accession 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 haveReferenceAmount (  ) const

Indicates presence of the reference_amount 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 haveReferenceDatabase (  ) const

Indicates presence of the reference_database 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 haveSelection (  ) const

Indicates presence of the selection 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.
ms_quant_average & operator= ( const ms_quant_average right )

C++ style assignment operator.

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

Set a custom value for the num_peptides attribute.

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

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

Set a custom value for the reference_accession attribute.

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

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

Set a custom value for the reference_amount attribute.

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

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

Set a custom value for the reference_database attribute.

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

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

Set a custom value for the selection attribute.

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

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 01:44:53