ms_mascotresults_params Class Reference [Mascot results file module]

Class which provides constructor parameters for either ms_peptidesummary or ms_proteinsummary. More...

#include <ms_mascotresults_params.hpp>

List of all members.

Public Member Functions
	ms_mascotresults_params (const unsigned int flags=ms_mascotresults::MSRES_GROUP_PROTEINS, double minProbability=0.05, int maxHitsToReport=0, const char *unigeneIndexFile=0, double ignoreIonsScoreBelow=0.0, int minPepLenInPepSummary=0, const char *singleHit=0, const unsigned int flags2=0)
	Call this method once to create the ms_mascotresults_params.
	ms_mascotresults_params (const ms_mascotresults_params &src)
	Copying constructor.
void	copyFrom (const ms_mascotresults_params *right)
	Copies all data from another instance of the class.
unsigned int	getFlags () const
	Returns the value of the flags parameter if available.
unsigned int	getFlags2 () const
	Returns the value of the flags2 parameter if available.
double	getIgnoreIonsScoreBelow () const
	Returns the value of the ignoreIonsScoreBelow parameter if available.
int	getMaxHitsToReport () const
	Returns the maximum number of protein hits to report.
int	getMinNumSigUniqueSequences () const
	Returns the value of the MinNumSigUniqueSequences parameter.
int	getMinPepLenInPeptideSummary () const
	Returns the minimum length of peptide match to use when generating a peptide summary report.
double	getMinProbability () const
	Returns the significance threshold.
std::string	getSingleHit () const
	Returns the optional single hit parameter used to get the results for a single hit quickly.
double	getTargetFDR () const
	Returns the target FDR, if any.
ms_mascotresults::DECOY_STATS_COUNT_TYPE	getTargetFDRType () const
	Returns the target FDR type.
std::string	getUnigeneIndexFile () const
	Optional file path to a UniGene Index file.
bool	isUsePeptideSummary () const
	Returns a hint as to whether a peptide or protein summary should be created.
ms_mascotresults_params &	operator= (const ms_mascotresults_params &right)
	Assignment operator.
void	setFlag (const ms_mascotresults::FLAGS flag, bool enabled)
	Toggles the value of an individual flag for use in the ms_mascotresults constructor.
void	setFlag2 (const ms_peptidesummary::MSPEPSUM flag, bool enabled)
	Toggles the value of an individual flag used in the ms_peptidesummary constructor.
void	setFlags (const unsigned int flags)
	Sets the value of the flags parameter for use in the ms_mascotresults constructor.
void	setFlags2 (const unsigned int flags2)
	Sets the value of the flags2 parameter used in the ms_peptidesummary constructor.
void	setIgnoreIonsScoreBelow (const double ignoreIonsScoreBelow)
	Sets the value of the ignoreIonsScoreBelow parameter.
void	setMaxHitsToReport (const int maxHitsToReport)
	Sets the maximum number of protein hits to report.
void	setMinNumSigUniqueSequences (const int n)
	Sets the value of the MinNumSigUniqueSequences parameter.
void	setMinPepLenInPeptideSummary (const int minPepLenInPeptideSummary)
	Sets the minimum length of peptide match to use when generating a peptide summary report.
void	setMinProbability (const double minProbability)
	Sets the significance threshold.
void	setSingleHit (const char *singleHit)
	Sets the optional single hit parameter.
void	setTargetFDR (double fdr)
	Sets the target FDR.
void	setTargetFDRType (ms_mascotresults::DECOY_STATS_COUNT_TYPE fdrType)
	Sets the target FDR type.
void	setUnigeneIndexFile (const char *unigeneIndexFile)
	Sets the optional file path to a UniGene Index file.
void	setUsePeptideSummary (const bool usePeptideSummary)
	Set the hint as to whether a peptide or protein summary should be created.

---

Detailed Description

Class which provides constructor parameters for either ms_peptidesummary or ms_proteinsummary.

---

Constructor & Destructor Documentation

ms_mascotresults_params	(	const unsigned int	flags = ms_mascotresults::MSRES_GROUP_PROTEINS,
		double	minProbability = 0.05,
		int	maxHitsToReport = 0,
		const char *	unigeneIndexFile = 0,
		double	ignoreIonsScoreBelow = 0.0,
		int	minPepLenInPepSummary = 0,
		const char *	singleHit = 0,
		const unsigned int	flags2 = 0
	)

Call this method once to create the ms_mascotresults_params.

This object has fields for all of the flags and parameters required to create peptide and protein summary result objects. Both ms_peptidesummary and ms_proteinsummary have constructors which will accept an ms_mascotresults_params object.

You do not need to supply any of the parameter values when creating an ms_mascotresults_params object as all of the parameters have setter methods, allowing you to update their values. You can also set all of the required parameters for a result by calling the get_ms_mascotresults_params method of ms_mascotresfile.

Parameters:

flags	can be one or more of the ms_mascotresults::FLAGS values OR'ed together
minProbability	specifies the significance threshold. See getMinProbability(). See also getTargetFDR().
maxHitsToReport	is a maximum value of protein hits to report. See getMaxHitsToReport().
unigeneIndexFile	is an optional file path to a UniGene Index file. This only makes sense if ms_mascotresults::MSRES_GROUP_PROTEINS is set. From programming languages other than C++, pass an empty string object to specify no UniGene index file.
ignoreIonsScoreBelow	is an optional flag for the peptide summary only. See getIgnoreIonsScoreBelow().
minPepLenInPepSummary	is an optional flag for the peptide summary only. Any peptides shorter than this will be ignored when grouping proteins (see Grouping proteins together).
singleHit	should only be used for getting the results for a single protein quickly. See setSingleHit().
flags2	should be one or more of the ms_peptidesummary::MSPEPSUM flags OR'd together

ms_mascotresults_params

(

const ms_mascotresults_params &

src )

Copying constructor.

Parameters:

src	is the source to initialise from

---

Member Function Documentation

void copyFrom

(

const ms_mascotresults_params *

right )

Copies all data from another instance of the class.

Parameters:

right

is the source to initialise from

unsigned int getFlags

(

)

const

Returns the value of the flags parameter if available.

The value of the flags parameter should be one or more of the ms_mascotresults::FLAGS values OR'ed together.

Returns:

The value of the flags parameter used by the ms_peptidesummary and ms_proteinsummary constructors

unsigned int getFlags2

(

)

const

Returns the value of the flags2 parameter if available.

Flags2 is an optional parameter for the peptide summary only. It's value should be one or more of the ms_peptidesummary::MSPEPSUM flags OR'ed together.

Returns:

The value of the flags2 parameter used by the ms_peptidesummary constructor.

double getIgnoreIonsScoreBelow

(

)

const

Returns the value of the ignoreIonsScoreBelow parameter if available.

ignoreIonsScoreBelow is an optional flag for the peptide summary only. Any peptides with a score less than this will be ignored. If the value is greater than 0 and less than 1 then this is assumed to to be a probability rather than an absolute score; the reciprocal of this value is passed to ms_peptidesummary::getPeptideThreshold() to determine the score cutoff.

A value of -1 is treated as equivalent to minProbability. This is the most convenient setting if you want to filter out non-significant matches.

If the search is an error tolerant search, any non-zero value is treated as equal to -1. That is, specifying IgnoreIonsScoreBelow = 0.0 will display all matches, and specifying any other value will display only significant matches.

Returns:

The value of ignoreIonsScoreBelow to use in the ms_peptidesummary constructor

int getMaxHitsToReport

(

)

const

Returns the maximum number of protein hits to report.

This is a maximum value. There may be fewer than this number if minProbability is low (or > 1 and high), or if there are insufficient results.

• If the ms_mascotresults::MSRES_MAXHITS_OVERRIDES_MINPROB flag is set, then the minProbability value is ignored when determining the number of hits to display.
• With versions of parser before Mascot 2.2, this flag was not available so a value of 0 was passed as minProbability in the standard Mascot results reports. Also, if this flag is specified, a value of zero can be used for maxHitsToReport and the cutoff is then specified by minProbability.
• If the flag ms_mascotresults::MSRES_GROUP_PROTEINS is set, then this value applies to the top level proteins -- the similar and subset proteins are not included in the count.

Returns:

The maximum number of protein hits to report.

int getMinNumSigUniqueSequences

(

)

const

Returns the value of the MinNumSigUniqueSequences parameter.

MinNumSigUniqueSequences is an optional flag for the peptide summary only. A protein hit must have at least as many significant unique sequences to be reported as a hit. A peptide sequence is significant if it has at least one peptide match above significance threshold, and it is unique if it appears in no other protein hit.

The default is 1. The value range is between 1 and 5, inclusive.

Returns:

The value of MinNumSigUniqueSequences to use in the ms_peptidesummary constructor

int getMinPepLenInPeptideSummary

(

)

const

Returns the minimum length of peptide match to use when generating a peptide summary report.

This is an optional flag for the peptide summary only. Any peptides shorter than this will be ignored when grouping proteins (see Grouping proteins together).

Returns:

the minimum peptide length used to differentiate different proteins.

double getMinProbability

(

)

const

Returns the significance threshold.

minProbability is applied to both peptide matches and protein hits.

Peptide matches:

• A peptide match (PSM) is significant if its expect value is below minProbability.
• minProbability can be overriden by getTargetFDR().

Protein hits if ms_mascotresults::MSRES_MAXHITS_OVERRIDES_MINPROB is active:

• If ms_mascotresults::MSRES_MAXHITS_OVERRIDES_MINPROB is set, minProbability is ignored. Instead, up to getMaxHitsToReport() proteins are reported.

Protein hits if MSRES_MAXHITS_OVERRIDES_MINPROB is not active:

• A value of 0 indicates no cutoff - report getMaxHitsToReport() proteins, whatever the protein scores.
• A value between 0 and 1 is used to calculate a protein score cut-off based on peptide match expect values. With standard protein scoring, 0.05 would discard all proteins with a score less the average score of a peptide with an expect value of 0.05. With MudPIT protein scoring, 0.05 would be the peptide expect value threshold used for calculating the protein scores, and only proteins with non-zero scores are reported.
• A value greater than 1 indicates an absolute score cutoff for proteins, but this is not valid for an Integrated error tolerant search and is not permitted in the standard Mascot Search reports, so is not recommended.
• If the flag ms_mascotresults::MSRES_GROUP_PROTEINS is set, then this value applies to the top level proteins - the similar and subset proteins are not 'cutoff' by this value.
• The cutoff point is the lower of maxHitsToReport and this value. With versions of parser before Mascot 2.2, MSRES_MAXHITS_OVERRIDES_MINPROB was not available so AUTO in the standard Mascot results reports was implemented by setting this probability to a (user) defined value and setting getMaxHitsToReport() to a very large number.

Other points to note:

• A value of less than 0 is not permitted and will be replaced with the default of 0.05.
• In Mascot Parser 2.2 and earlier, a value between 0.1 and 1.0 was replaced with the default value of 0.05. In Mascot Parser 2.3, any value between 1e-18 and 1.0 is acceptable.

Returns:

The value of the minProbability parameter used in the ms_peptidesummary and ms_proteinsummary constructors

std::string getSingleHit

(

)

const

Returns the optional single hit parameter used to get the results for a single hit quickly.

Should only be used for getting the results for a single protein quickly. See setSingleHit().

Returns:

The single hit parameter value if available.

double getTargetFDR

(

)

const

Returns the target FDR, if any.

Target FDR is only valid with ms_peptidesummary. Target FDR type is PSM by default, which can be overriden using setTargetFDRType().

If target FDR is 0 (default), it is interpreted as "not set". ms_peptidesummary uses getMinProbability() as the significance threshold.

Target FDR is a value between 0 and 1. If the search is a target-decoy search, ms_peptidesummary tries to calibrate minProbability to a value that yields the target FDR (either PSM FDR or sequence FDR). If the search is not a target-decoy search, or ms_peptidesummary fails to reach the target, then getMinProbability() is used as the fallback value.

If the search is a target-decoy, integrated error tolerant, ms_peptidesummary has two independent significance thresholds, one for first pass matches and one for second pass matches. If target FDR is non-zero, ms_peptidesummary tries to calibrate both sets of matches to the same target FDR.

Mascot Server 2.8 and later may output a first_pass_threshold= value in the header section of the results file. This is the minProbability used at the end of the first pass of an integrated error tolerant search.

Mascot Server 2.8 and later accept a TARGET_FDR_PERCENT= search parameter, which is stored in the parameters section of the results file.

ms_mascotresfile::get_ms_mascotresults_params() follows this protocol:

• Use ms_mascotresfile::getSectionValueDouble() to get first_pass_threshold=.
• If it's non-zero, pass it to setMinProbability().
• Use ms_searchparams::getTARGET_FDR_PERCENT(). Divide by 100 and pass to setTargetFDR().
• Set FDR type to the default (ms_mascotresults::DS_COUNT_PSM).

Returns:

target FDR, or 0 if not set.

ms_mascotresults::DECOY_STATS_COUNT_TYPE getTargetFDRType

(

)

const

Returns the target FDR type.

Target FDR type can be either PSM (default) or sequence.

PSM FDR is calculated from the number of decoy PSMs and target PSMs.

Sequence FDR is calculated from the number of distinct decoy peptide sequences and distinct target peptide sequences, where each distinct peptide sequence has at least one PSM.

See getTargetFDR() for more details.

Returns:

target FDR type.

std::string getUnigeneIndexFile

(

)

const

Optional file path to a UniGene Index file.

This only makes sense if ms_mascotresults::MSRES_GROUP_PROTEINS is set.

Returns:

The unigene index file parameter if available.

bool isUsePeptideSummary

(

)

const

Returns a hint as to whether a peptide or protein summary should be created.

The parameter is set when you call get_ms_mascotresults_params to populate the ms_mascotresults_params object. The value returned by this function is not used by any of the ms_peptidesummary or ms_proteinsummary constructors.

Returns:

True if the ms_mascotresfile contains any MS/MS data, false if not.

ms_mascotresults_params & operator=

(

const ms_mascotresults_params &

right )

Assignment operator.

Parameters:

right

is the source to initialise from

Returns:

reference to the current object

void setFlag	(	const ms_mascotresults::FLAGS	flag,
		bool	enabled
	)

Toggles the value of an individual flag for use in the ms_mascotresults constructor.

Parameters:

flag	Should be one of the ms_mascotresults::FLAGS values.
enabled	Choose true to set the flag and false to unset.

void setFlag2	(	const ms_peptidesummary::MSPEPSUM	flag,
		bool	enabled
	)

Toggles the value of an individual flag used in the ms_peptidesummary constructor.

Parameters:

flag	Should be one of the ms_peptidesummary::MSPEPSUM values.
enabled	Choose true to set the flag and false to unset.

void setFlags

(

const unsigned int

flags )

Sets the value of the flags parameter for use in the ms_mascotresults constructor.

Parameters:

flags

Should be one or more of the ms_mascotresults::FLAGS values OR'ed together.

void setFlags2

(

const unsigned int

flags2 )

Sets the value of the flags2 parameter used in the ms_peptidesummary constructor.

Flags2 is an optional parameter for the peptide summary only.

Parameters:

flags2

Should be one or more of the ms_peptidesummary::MSPEPSUM flags OR'ed together.

void setIgnoreIonsScoreBelow

(

const double

ignoreIonsScoreBelow )

Sets the value of the ignoreIonsScoreBelow parameter.

Parameters:

ignoreIonsScoreBelow

is an optional flag for the peptide summary only. Any peptides with a score less than this will be ignored. If the value is greater than 0 and less than 1 then this is assumed to to be a probability rather than an absolute score; the reciprocal of this value is passed to ms_peptidesummary::getPeptideThreshold() to determine the score cutoff. If the value is -1, it is treated as equivalent to minProbability.

void setMaxHitsToReport

(

const int

maxHitsToReport )

Sets the maximum number of protein hits to report.

For details, see getMaxHitsToReport().

Parameters:

maxHitsToReport

is the new maximum value.

void setMinNumSigUniqueSequences

(

const int

n )

Sets the value of the MinNumSigUniqueSequences parameter.

For details, see getMinNumSigUniqueSequences().

Parameters:

n	New value between 1 and 5, inclusive. If n is outside this range, it's set to 1.

void setMinPepLenInPeptideSummary

(

const int

minPepLenInPeptideSummary )

Sets the minimum length of peptide match to use when generating a peptide summary report.

Parameters:

minPepLenInPeptideSummary

is an optional flag for the peptide summary only. Any peptides shorter than this will be ignored when grouping proteins (see Grouping proteins together).

void setMinProbability

(

const double

minProbability )

Sets the significance threshold.

For details, see getMinProbability() and getTargetFDR().

Parameters:

minProbability

specifies the significance threshold.

void setSingleHit

(

const char *

singleHit )

Sets the optional single hit parameter.

Parameters:

singleHit

should only be used for getting the results for a single protein quickly. This is used for example by the the protein view report in Mascot, which just shows the matches for a single protein. See Using the singleHit parameter to return a single protein. From programming languages other than C++, pass an empty string object to specify that all proteins should be used. For Mascot 2.3 and later, a database index needs to be specified because the search may have been against multiple fasta files. If the database index is to be specified, the string must be of the form: "3:CH60_SHEON" and the ms_peptidesummary::MSPEPSUM_SINGLE_HIT_DBIDX must be specified in flags2. Othersise, at database index of 1 is assumed.

void setTargetFDR

(

double

fdr )

Sets the target FDR.

Target FDR is a value between 0 and 1. Zero means "not set" and is the default. Target FDR type is set with setTargetFDRType().

See getTargetFDR() for details.

Parameters:

fdr	target FDR. If outside the valid range, target FDR is set to 0.

void setTargetFDRType

(

ms_mascotresults::DECOY_STATS_COUNT_TYPE

fdrType )

Sets the target FDR type.

Target FDR type can be either PSM (default) or sequence.

See getTargetFDRType() for details.

Parameters:

fdrType

new type.

void setUnigeneIndexFile

(

const char *

unigeneIndexFile )

Sets the optional file path to a UniGene Index file.

Parameters:

unigeneIndexFile

is an optional file path to a UniGene Index file. This only makes sense if ms_mascotresults::MSRES_GROUP_PROTEINS is set. From programming languages other than C++, pass an empty string object to specify no UniGene index file.

void setUsePeptideSummary

(

const bool

usePeptideSummary )

Set the hint as to whether a peptide or protein summary should be created.

The parameter is set when you call get_ms_mascotresults_params to populate the ms_mascotresults_params object. The value returned by this function is not used by any of the ms_peptidesummary or ms_proteinsummary constructors.

Parameters:

usePeptideSummary

Pass in true if the result file contains MS/MS data, false if not

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

• ms_mascotresults_params.hpp
• ms_mascotresults_params.cpp