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>

List of all members.

Public Types
enum	eGrouping {   eGroupAuto = 0,   eGroupStandard = 1,   eGroupFamily = 2 }
	Setting to control how proteins are grouped. More...
enum	eScoring {   eAuto = 0,   eMudpit = 1,   eStandard = 99999999 }
	Determine whether to use MudPIT or standard (pre-Mascot 2.2) scoring. More...
enum	eSpectralLibrary {   eUnknown = -1,   eFASTA = 0,   eLibrary = 1,   eIntegrated = 2 }
	For integrated FASTA and Spectral Library search, determines the default result display option. More...
Public Member Functions
	ms_distiller_data_search ()
	Default constructor.
	ms_distiller_data_search (const std::string &taskId, bool isLoaded, const std::string &cacheFileName, const std::string &quantMethodXml, const std::string &mascotServerURL, const std::string &mascotServerVersion, unsigned int flags, unsigned int flags2, bool requireBoldRed, bool showSameset, double showSubset, bool loadUnassigned, double significanceThreshold, eScoring scoring, int reporttop, bool errTolPeptide, eGrouping proteinGrouping, bool percolator, double scoreExpectCutOff, bool showSamesetFamily, bool showSubsetFamily, eSpectralLibrary libraryDisplayOption, bool percolatorUseProteins, bool percolatorUseRT, int minPepLenInPepSummary)
	Constructor with all values.
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.
std::string	getMascotSearchURL (const std::string &resultsFilePath) const
	Return the URL for the search on the Mascot Server.
std::string	getMascotServerURL () const
	The URL for the Mascot Server.
int	getMinPepLenInPepSummary () const
	Return the minimum length of a peptide to be shown in a peptide summary.
unsigned int	getPeptideSummaryFlags () const
	Return the default flags values to pass to the peptide summary constructor (as used in Distiller).
unsigned	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.
bool	getPercolatorUseProteins () const
	Return true if percolator is set to set proteins for 'scoring'.
bool	getPercolatorUseRT () const
	Return true if percolator will calculate and use retention times.
eGrouping	getProteinGrouping () const
	Return the method of protein grouping that was used.
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.
eSpectralLibrary	getSpectralLibraryDisplayOption () const
	Returns the spectral library display option for the report.
std::string	getTaskId () const
	The task ID of the Mascot search.
bool	serverVersionNewerOrSameAs (int major, int minor, int patch) const
	Compare the version of the Mascot Server with the specified values.

---

Detailed Description

The details of a Distiller search.

A list of these is stored in XML in the rover_data file in the Distiller project file. The data comes from the relevant <MascotSearch> section inside the <mascotsearches> section. Call ms_distiller_data::getSearch to get an instance of this object

---

Member Enumeration Documentation

enum eGrouping

Setting to control how proteins are grouped.

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

Enumerator:

eGroupAuto	Grouping automatically determined when grouping begins, this value never appears in results.
eGroupStandard	Standard grouped protein list using parsimony / Occam’s razor.
eGroupFamily	Protein family grouping using Hierarchical Clustering.

enum eScoring

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

See Using enumerated values and static const ints 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.

enum eSpectralLibrary

For integrated FASTA and Spectral Library search, determines the default result display option.

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

Enumerator:

eUnknown	Attribute was not set.
eFASTA	Display FASTA search results only.
eLibrary	Display spectral library results only.
eIntegrated	Display integrated results report.

---

Constructor & Destructor Documentation

ms_distiller_data_search	(	const std::string &	taskId,
		bool	isLoaded,
		const std::string &	cacheFileName,
		const std::string &	quantMethodXml,
		const std::string &	mascotServerURL,
		const std::string &	mascotServerVersion,
		unsigned int	flags,
		unsigned int	flags2,
		bool	requireBoldRed,
		bool	showSameset,
		double	showSubset,
		bool	loadUnassigned,
		double	significanceThreshold,
		eScoring	scoring,
		int	reporttop,
		bool	errTolPeptide,
		eGrouping	proteinGrouping,
		bool	percolator,
		double	scoreExpectCutOff,
		bool	showSamesetFamily,
		bool	showSubsetFamily,
		eSpectralLibrary	libraryDisplayOption,
		bool	percolatorUseProteins,
		bool	percolatorUseRT,
		int	minPepLenInPepSummary
	)

Constructor with all values.

Parameters:

taskId	comes from the TaskID attribute in the <MascotSearch> element
isLoaded	comes from the Loaded attribute in the <MascotSearch> element
cacheFileName	comes from the cacheFileName attribute in the <MascotSearch> element
quantMethodXml	comes from the quantMethod attribute in the <MascotImportOptions> element
mascotServerURL	comes from the URL attribute in the <Server> element for the 'Default' server in the <MascotServers> element
mascotServerVersion	comes from the Version attribute in the <Server> element for the 'Default' server in the <MascotServers> element
flags	are the ms_mascotresults::FLAGS that would be passed to a ms_peptidesummary constructor
flags2	are the ms_peptidesummary::MSPEPSUM flags that would be passed to a ms_peptidesummary constructor
requireBoldRed	comes from the requireBoldRed attribute in the <blueOptions>
showSameset	comes from the showSameset attribute in the <blueOptions>
showSubset	comes from the showSubset attribute in the <blueOptions>
loadUnassigned	comes from the loadUnassignedList attribute in the <blueOptions>
significanceThreshold	comes from the significanceThresholdStr attribute in the <blueOptions>
scoring	comes from the scoringType attribute in the <blueOptions>
reporttop	comes from the reportTop attribute in the <blueOptions>
errTolPeptide	comes from the ErrTolPeptide attribute in the <blueOptions>
proteinGrouping	comes from the proteinGrouping attribute in the <blueOptions>
percolator	comes from the percolator attribute in the <blueOptions>
scoreExpectCutOff	comes from the ScoreExpectCutOff attribute in the <blueOptions>
showSamesetFamily	comes from the showSamesetFamily attribute in the <blueOptions>
showSubsetFamily	comes from the showSubsetFamily attribute in the <blueOptions>
libraryDisplayOption	comes from the spectralLibraryDisplayOption attribute in the <blueOptions>
percolatorUseProteins	comes from the percolatorUseProteins attribute in the <blueOptions>
percolatorUseRT	comes from the percolatorUseRT attribute in the <blueOptions>
minPepLenInPepSummary	comes from the minPepLenInPepSummary attribute in the <blueOptions>

---

Member Function Documentation

std::string getCacheFileName

(

)

const

Return the name of the cache file used by Parser.

Default value: empty string

Obtained from the cacheFileName attribute in the <MascotSearch> element.

Returns:

The name of the cache file used by Parser.

bool getErrTolPeptide

(

)

const

Return true if the peptide search used error tolerant matching.

Default value: false

Obtained from the ErrTolPeptide attribute in the <blueoptions> element.

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.

Default value: false

Obtained from the Loaded attribute in the <MascotSearch> element.

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.

Default value: false

Obtained from the loadUnassignedList attribute in the <blueoptions> element.

Returns:

True if the unassigned list should be loaded, false if not.

std::string getMascotSearchURL

(

const std::string &

resultsFilePath )

const

Return the URL for the search on the Mascot Server.

Default value: empty string

Built up on the fly from all the settings.

The URL will always specify master_results_2.pl rather than master_results.pl, even for a PMF

Parameters:

resultsFilePath

is, for example: "../data/2018010/F0012345.dat"

Returns:

the URL for the search on the Mascot Server

int getMinPepLenInPepSummary

(

)

const

Return the minimum length of a peptide to be shown in a peptide summary.

Default value: 5

Obtained from the minPepLenInPepSummary attribute in the <blueoptions> element which was added in Parser 2.7

Returns:

the minimum length of a peptide to be shown in a peptide summary

unsigned 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.

Ideally, this function would call ms_mascotresfile::get_ms_mascotresults_params but we don't have a ms_mascotresfile object available.

Returns:

The peptide summary flags settings.

unsigned 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.

Default value: false

Obtained from the percolator attribute in the <blueoptions> element.

Returns:

True if percolator re-scoring was used.

bool getPercolatorUseProteins

(

)

const

Return true if percolator is set to set proteins for 'scoring'.

Default value: false

Obtained from the percolatorUseProteins attribute in the <blueoptions> element which was added in Parser 2.7

Returns:

true if percolator is set to set proteins for 'scoring'

bool getPercolatorUseRT

(

)

const

Return true if percolator will calculate and use retention times.

Default value: false

Obtained from the percolatorUseRT attribute in the <blueoptions> element which was added in Parser 2.7

Returns:

true if percolator will calculate and use retention times.

ms_distiller_data_search::eGrouping getProteinGrouping

(

)

const

Return the method of protein grouping that was used.

Default value: ms_distiller_data_search::eGroupAuto

Obtained from the proteinGrouping attribute in the <blueoptions> element.

Returns:

The method of protein grouping that was used.

std::string getQuantMethodXml

(

)

const

The XML text for the quantitation method, if any.

Default value: empty string

Obtained from the quantMethod attribute in the <MascotImportOptions> element.

This text can be loaded into a ms_quant_configfile using ms_quant_configfile::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.

Default value: 0

Obtained from the reportTop attribute in the <blueoptions> element.

Returns:

The number of protein hits to include in the results.

bool getRequireBoldRed

(

)

const

Return true if bold, red font should be used.

Default value: false

Obtained from the requireBoldRed attribute in the <blueoptions> element.

Returns:

True if bold, red font should be used.

double getScoreExpectCutOff

(

)

const

Return the score cutoff threshold value.

Default value: 0

Obtained from the ScoreExpectCutOff attribute in the <blueoptions> element.

Returns:

The score cutoff threshold value.

ms_distiller_data_search::eScoring getScoring

(

)

const

Return the method of scoring that was used.

Default value: ms_distiller_data_search::eAuto

Obtained from the scoringType attribute in the <blueoptions> element.

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.

Default value: true

Obtained from the showSameset attribute in the <blueoptions> element.

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.

Default value: true

Obtained from the showSamesetFamily attribute in the <blueoptions> element.

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.

Default value: 0

Obtained from the showSubset attribute in the <blueoptions> element. This value is base 64 eoncoded in the xml file.

Returns:

The threshold used to determine if a subset should be shown.

bool getShowSubsetFamily

(

)

const

Return true if family subsets should be shown.

Default value: false

Obtained from the showSubsetFamily attribute in the <blueoptions> element.

Returns:

True if family subsets should be shown.

double getSignificanceThreshold

(

)

const

Return the minimum probabilty threshold in use.

Default value:

Obtained from the significanceThreshold attribute in the <blueoptions> element which is a base 64 encoded value. If that isn't present, get the value from the significanceThresholdStr attribute.

Returns:

The minimum probability threshold setting.

ms_distiller_data_search::eSpectralLibrary getSpectralLibraryDisplayOption

(

)

const

Returns the spectral library display option for the report.

Default value: ms_distiller_data_search::eUnknown

Obtained from the spectralLibraryDisplayOption attribute in the <blueoptions> element which was added in Parser 2.7.

The value in the XML should be one of: "fasta", "library" or "integrated".

Returns:

The spectral library results display option

std::string getTaskId

(

)

const

The task ID of the Mascot search.

Default value: empty string

Obtained from the TaskID attribute in the <MascotSearch> element.

Returns:

The task ID of the Mascot search.

bool serverVersionNewerOrSameAs	(	int	major,
		int	minor,
		int	patch
	)		const

Compare the version of the Mascot Server with the specified values.

Parameters:

major	is, for example 2 for version 2.5.1
minor	is, for example 5 for version 2.5.1
patch	is, for example 1 for version 2.5.1

Returns:

true if the version saved in this object is a newer version than the passed major and minor values passed

---

The documentation for this class was generated from the following files:

• ms_distiller_data_search.hpp
• ms_distiller_data_search.cpp