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

The details of a Distiller search. More...

#include <ms_distiller_data_search.hpp>

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List of all members.

Public Types

enum  eGrouping {
  eGroupAuto = 0,
  eGroupStandard = 1,
  eGroupFamily = 2
}
 

Setting to control how proteins are grouped.

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enum  eScoring {
  eAuto = 0,
  eMudpit = 1,
  eStandard = 99999999
}
 

Determine whether to use MudPIT or standard (pre-Mascot 2.2) scoring.

More...

Public Member Functions

std::string getCacheFileName () const
 Return the name of the cache file used by Parser.
bool getErrTolPeptide () const
 Return true if the peptide search used error tolerant matching.
bool getLoaded () const
 Returns true if the search data was currently loaded when the Distiller data was saved.
bool getLoadUnassigned () const
 Return true if the unassigned list should be loaded when opening the result.
int getPeptideSummaryFlags () const
 Return the default flags values to pass to the peptide summary constructor (as used in Distiller).
int getPeptideSummaryFlags2 () const
 Return the default flags2 values to pass to the peptide summary constructor (as used in Distiller).
bool getPercolator () const
 Return true if the percolator is in use.
eGrouping getProteinGrouping () const
 Return the method of protein grouping that was used.
const
matrix_science::ms_quant_configfile
getQuantConfigFile () const
 Return the quantitation configuration information.
std::string getQuantMethodXml () const
 The XML text for the quantitation method, if any.
int getReporttop () const
 Return the number of protein hits to include in the results.
bool getRequireBoldRed () const
 Return true if bold, red font should be used.
double getScoreExpectCutOff () const
 Return the score cutoff threshold value.
eScoring getScoring () const
 Return the method of scoring that was used.
bool getShowSamesets () const
 Return true if same set matches should be shown for peptide and protein summary reports.
bool getShowSamesetsFamily () const
 Return true if same set matches should be shown for protein family summary reports.
double getShowSubset () const
 Return the threshold used to determine if a subset should be shown.
bool getShowSubsetFamily () const
 Return true if family subsets should be shown.
double getSignificanceThreshold () const
 Return the minimum probabilty threshold in use.
std::string getTaskId () const
 The task ID of the Mascot search.

Detailed Description

The details of a Distiller search.

A list of these is stored in XML in the Distiller project file.


Member Enumeration Documentation

enum eGrouping

Setting to control how proteins are grouped.

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

Enumerator:
eGroupAuto 

Grouping automatically determined when grouping begins, this value never appears in results.

eGroupStandard 

Non-grouped protein list.

eGroupFamily 

protein family grouping

enum eScoring

Determine whether to use MudPIT or standard (pre-Mascot 2.2) scoring.

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

Enumerator:
eAuto 

Use MudPIT when the ratio of the number of spectra to the number of entries in the database is greater than the threshold.

eMudpit 

Always use MudPIT.

eStandard 

Never use MudPIT.


Member Function Documentation

std::string getCacheFileName (  ) const

Return the name of the cache file used by Parser.

Returns:
The name of the cache file used by Parser.
bool getErrTolPeptide (  ) const

Return true if the peptide search used error tolerant matching.

Returns:
True if the peptide result was generated by an error tolerant Mascot search.
bool getLoaded (  ) const

Returns true if the search data was currently loaded when the Distiller data was saved.

Returns:
True if the search was loaded when the Distiller data was saved.
bool getLoadUnassigned (  ) const

Return true if the unassigned list should be loaded when opening the result.

Returns:
True if the unassigned list should be loaded, false if not.
int getPeptideSummaryFlags (  ) const

Return the default flags values to pass to the peptide summary constructor (as used in Distiller).

The flags settings are a collection of values, bitwise or-ed together, from the FLAGS enumeration of ms_mascotresults.

Returns:
The peptide summary flags settings.
int getPeptideSummaryFlags2 (  ) const

Return the default flags2 values to pass to the peptide summary constructor (as used in Distiller).

The flags2 settings are a collection of values, bitwise or-ed together, from the MSPEPSUM enumeration of ms_peptidesummary.

Returns:
The peptide summary flags2 settings.
bool getPercolator (  ) const

Return true if the percolator is in use.

Returns:
True if percolator re-scoring was used.
ms_distiller_data_search::eGrouping getProteinGrouping (  ) const

Return the method of protein grouping that was used.

Returns:
The method of protein grouping that was used.
const matrix_science::ms_quant_configfile & getQuantConfigFile (  ) const

Return the quantitation configuration information.

Returns:
The quantitation configuration information.
std::string getQuantMethodXml (  ) const

The XML text for the quantitation method, if any.

This text can be loaded into a ms_quant_configfile using read_buffer().

Returns:
The XML text containing the quantitation method, if any.
int getReporttop (  ) const

Return the number of protein hits to include in the results.

Returns:
The number of protein hits to include in the results.
bool getRequireBoldRed (  ) const

Return true if bold, red font should be used.

Returns:
True if bold, red font should be used.
double getScoreExpectCutOff (  ) const

Return the score cutoff threshold value.

Returns:
The score cutoff threshold value.
ms_distiller_data_search::eScoring getScoring (  ) const

Return the method of scoring that was used.

Returns:
The method of scoring that was used.
bool getShowSamesets (  ) const

Return true if same set matches should be shown for peptide and protein summary reports.

Returns:
True if same set protein matches should be displayed, false if not
bool getShowSamesetsFamily (  ) const

Return true if same set matches should be shown for protein family summary reports.

Returns:
True if same set protein matches should be displayed, false if not
double getShowSubset (  ) const

Return the threshold used to determine if a subset should be shown.

Returns:
The threshold used to determine if a subset should be shown.
bool getShowSubsetFamily (  ) const

Return true if family subsets should be shown.

Returns:
True if family subsets should be shown.
double getSignificanceThreshold (  ) const

Return the minimum probabilty threshold in use.

Returns:
The minimum probability threshold setting.
std::string getTaskId (  ) const

The task ID of the Mascot search.

Returns:
The task ID of the Mascot search.

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 01:44:52