Matrix Science header
Public Member Functions

ms_quant_normalisation Class Reference
[Mascot configuration files module]

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

#include <ms_quant_normalisation.hpp>

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List of all members.

Public Member Functions

 ms_quant_normalisation ()
 Default constructor.
 ms_quant_normalisation (const ms_quant_normalisation &src)
 Copying constructor.
virtual ~ms_quant_normalisation ()
 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_normalisation *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 dropMethod ()
 Delete the method attribute.
void dropPeptides ()
 Delete the peptides element.
void dropProteins ()
 Delete the proteins element.
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.
const
ms_quant_normalisation_peptides
getPeptides () const
 Returns a pointer to the peptides element.
std::string getPeptidesSchemaType () const
 Obtain a symbolic name for the peptides element schema type.
const
ms_quant_normalisation_proteins
getProteins () const
 Returns a pointer to the proteins element.
std::string getProteinsSchemaType () const
 Obtain a symbolic name for the proteins element schema type.
virtual std::string getSchemaType () const
 Returns name of the schema type that can be used to validate this element.
bool haveMethod () const
 Indicates presence of the method attribute.
bool havePeptides () const
 Indicates presence of the peptides element.
bool haveProteins () const
 Indicates presence of the proteins element.
ms_quant_normalisationoperator= (const ms_quant_normalisation &right)
 C++ style assignment operator.
void setMethod (const char *value)
 Set a custom value for the method attribute.
void setPeptides (const ms_quant_normalisation_peptides *peptides)
 Supply custom content for peptides element.
void setProteins (const ms_quant_normalisation_proteins *proteins)
 Supply custom content for the proteins element.
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 normalisation element in quantitation.xml.

Method of normalising ratios for a complete data set.


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_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_normalisation 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 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 dropMethod (  )

Delete the method attribute.

Disables the attribute until it is re-set.

void dropPeptides (  )

Delete the peptides element.

Deletes the element until it is re-set.

void dropProteins (  )

Delete the proteins element.

Deletes the element until it is re-set.

std::string getMethod (  ) const

Returns the value of the method attribute.

  • Average: For each ratio, the geometric mean of all reported values for peptide matches is made unity.
  • Median: For each ratio, the median of all reported values for peptide matches is made unity.
  • Sum: (Reporter protocol only) The total intensity of each reporter ion, summed across all MS/MS spectra, is made equal.

Sum is only available for reporter protocol; average and median are only available when all protein hits are processed (i.e. REPORT=AUTO).

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.
const ms_quant_normalisation_peptides * getPeptides (  ) const

Returns a pointer to the peptides element.

List of peptide sequences to be used for normalisation.

Returns:
a read-only pointer to an object with the current element content. See Maintaining object references: two rules of thumb.
std::string getPeptidesSchemaType (  ) const

Obtain a symbolic name for the peptides 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.
const ms_quant_normalisation_proteins * getProteins (  ) const

Returns a pointer to the proteins element.

List of protein accessions to be used for normalisation.

Returns:
a read-only pointer to an object with the current element content. See Maintaining object references: two rules of thumb.
std::string getProteinsSchemaType (  ) const

Obtain a symbolic name for the proteins 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 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 havePeptides (  ) const

Indicates presence of the peptides element.

Returns:
TRUE if the element is present and FALSE otherwise.
bool haveProteins (  ) const

Indicates presence of the proteins element.

Returns:
TRUE if the element is present and FALSE otherwise.
ms_quant_normalisation & operator= ( const ms_quant_normalisation right )

C++ style assignment operator.

Parameters:
rightanother instance of this class to copy the content from.
Returns:
reference to the current object
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 setPeptides ( const ms_quant_normalisation_peptides peptides )

Supply custom content for peptides element.

Parameters:
peptidesa new content for the element.
void setProteins ( const ms_quant_normalisation_proteins proteins )

Supply custom content for the proteins element.

Parameters:
proteinsa new content for the element.
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