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Public Types | Public Member Functions | Static Public Member Functions

ms_ms1quant_match_ratio Class Reference
[Quantitation analysis for Mascot Server and Distiller]

The status resulting ratio for a peptide found in a match. More...

#include <ms_ms1quant_match_ratio.hpp>

Inherits matrix_science::ms_handle.

List of all members.

Public Types

enum  ratioStatusCode {
  RS_EMPTY = 0,
  RS_OK = 1,
  RS_ISOLATEDPRECURSORFAILED = 2,
  RS_INTEFERENCEFAILED = 4,
  RS_NODATA = 8,
  RS_FITEXYSIGMA = 16,
  RS_NEGATIVERATIO = 32,
  RS_INFINITERATIO = 64,
  RS_ZERORATIO = 128,
  RS_OUTLIER = 256
}
 

Status codes from fitting ratios.

More...

Public Member Functions

 ms_ms1quant_match_ratio ()
 Default constructor.
 ms_ms1quant_match_ratio (const ms_ms1quant_match_ratio_body &body)
 Populated constructor, linked to loaded data.
bool getFitexy (ms_fitexy_result &value) const
 Get the fitexy value. Returns true if a fitexy value is set.
double getQuality () const
 Get the quality of the match.
std::string getRatioName () const
 Returns the ratio name.
int getStatus () const
 Get the status composite value.
std::vector< ratioStatusCodegetStatusList () const
 Get the status values. Each status in the list is a single bit.
double getValue () const
 Return the numerical value of the ratio.
bool isIncluded () const
 Returns true if the item should be included in calculations.
bool isSet () const
 Returns true if the item has a value set.
bool isUsedForAverage () const
 Returns true if the item is used in the average protocol for quantitation.
bool isValid () const
 Returns true if the item has a valid value.

Static Public Member Functions

static ratioStatusCode getCodeFromXml (std::string text)
 Get the status code for an XML attribute value.
static bool getCodeInfo (ratioStatusCode code, const ms_quant_method &method, double &info)
 Return true if the status is associated with further information.
static std::string getXmlCode (ratioStatusCode code)
 Get the XML attribute value for a status code.

Detailed Description

The status resulting ratio for a peptide found in a match.

This is stored in XML in a "originalRatio" entity.


Member Enumeration Documentation

Status codes from fitting ratios.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
RS_EMPTY 

no status set

RS_OK 

ok

RS_ISOLATEDPRECURSORFAILED 

isolated precursor failed [extra information is option value 'isolated precursor threshold']

RS_INTEFERENCEFAILED 

inteference failed [extra information is option value 'matched rho']

RS_NODATA 

no data

RS_FITEXYSIGMA 

fitexy sigma [extra information is option value 'elution profile correlation threshold']

RS_NEGATIVERATIO 

negative ratio

RS_INFINITERATIO 

infinite ratio

RS_ZERORATIO 

zero ratio

RS_OUTLIER 

outlier


Constructor & Destructor Documentation

Default constructor.

Assigns reasonable default values to all internal members.

ms_ms1quant_match_ratio ( const ms_ms1quant_match_ratio_body &  body )

Populated constructor, linked to loaded data.

Parameters:
bodyThe data loaded from the result file.

Member Function Documentation

matrix_science::ms_ms1quant_match_ratio::ratioStatusCode getCodeFromXml ( std::string  text ) [static]

Get the status code for an XML attribute value.

Parameters:
textThe string used to encode the ratio status in the XML file.
Returns:
The ratio status corresponding to the XML encoded string.
bool getCodeInfo ( ratioStatusCode  code,
const ms_quant_method method,
double &  info 
) [static]

Return true if the status is associated with further information.

Three status codes have further information associated with them:

  • RS_ISOLATEDPRECURSORFAILED: isolated precursor threshold.
  • RS_INTEFERENCEFAILED: matched rho.
  • RS_FITEXYSIGMA: elution profile correlation threshold.
Parameters:
codeThe ratio status for which extra information is wanted.
methodThe quantitation method.
infoFilled in with the value of the extra information.
Returns:
True if there is extra information for this ratio status.
bool getFitexy ( matrix_science::ms_fitexy_result value ) const

Get the fitexy value. Returns true if a fitexy value is set.

Parameters:
valueFilled in with the ms_fitexy_result, if any.
Returns:
True if a fitexy value is set.
double getQuality (  ) const

Get the quality of the match.

Std. Err. = sigb / abs(b) from fitexy. Perfect fit is 0.0.

Returns:
The quality of the ratio.
std::string getRatioName (  ) const

Returns the ratio name.

Returns:
The ratio name.
int getStatus (  ) const

Get the status composite value.

Whether a peptide ratio is included or rejected when calculating a protein ratio.

These can be retrieved as a collection of separate values with getStatusList().

Returns:
A bitwise OR of any number of ratioStatusCode values.
std::vector< ms_ms1quant_match_ratio::ratioStatusCode > getStatusList (  ) const

Get the status values. Each status in the list is a single bit.

These can be retrieved as a single composite value with getStatus().

Returns:
A collection of the individual status values.
double getValue (  ) const

Return the numerical value of the ratio.

Returns:
The value of the ratio.
std::string getXmlCode ( ratioStatusCode  code ) [static]

Get the XML attribute value for a status code.

Parameters:
codeThe ratio status to get the XML excoding string for.
Returns:
The string used to encode the ratio status in the XML file.
bool isIncluded (  ) const

Returns true if the item should be included in calculations.

Returns:
True if the item should be included in calculations.
bool isSet (  ) const

Returns true if the item has a value set.

Returns:
True if the item has a value set.
bool isUsedForAverage (  ) const

Returns true if the item is used in the average protocol for quantitation.

The Average protocol only uses a number of the the most intense peptides.

Returns:
True if the item has been used in the Average protocol calculations.
bool isValid (  ) const

Returns true if the item has a valid value.

Returns:
True if the item has a valid value.

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