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Public Member Functions

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.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.
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 getMinPepLenInPeptideSummary () const
 Returns the minimum length of peptide match to use when generating a peptide summary report.
double getMinProbability () const
 Returns the probabilty cutoff point for protein scores, a cutoff for an Integrated error tolerant search and a threshold for calculating mudpit scores.
std::string getSingleHit () const
 Returns the optional single hit parameter used to get the results for a single hit quickly.
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.
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 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 probabilty cutoff point for protein scores, a cutoff for an Integrated error tolerant search and a threshold for calculating mudpit scores.
void setSingleHit (const char *singleHit)
 Sets the optional single hit parameter.
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 ms_mascotresfile::get_ms_mascotresults_params(const ms_mascotoptions & opts, ms_mascotresults_params & params) method of ms_mascotresfile.

Parameters:
flagscan be one or more of the ms_mascotresults::FLAGS values OR'ed together
minProbabilityspecifies a cutoff point for protein scores, a cutoff for an Integrated error tolerant search and a threshold for calculating mudpit scores.

  • A value of 0 indicates no cutoff - report maxHitsToReport 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. This value is also used to select proteins for an Integrated error tolerant search.
  • 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.
  • 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.

Other points to note:

  • 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, unless the ms_mascotresults::MSRES_MAXHITS_OVERRIDES_MINPROB flag is set. With versions of parser before Mascot 2.2, this flag was not available so AUTO in the standard Mascot results reports was implemented by setting this probablility to a (user) defined value and setting maxHitsToReport to a very large number.
maxHitsToReportis 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.
unigeneIndexFileis 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.
ignoreIonsScoreBelowis 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 getPeptideThreshold() to determine the score cutoff.
minPepLenInPepSummaryis an optional flag for the peptide summary only. Any peptides shorter than this will be ignored when grouping proteins (see Grouping proteins together).
singleHitshould 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.
flags2should be one or more of the ms_peptidesummary::MSPEPSUM flags OR'd together

Member Function Documentation

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.

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 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 probabilty cutoff point for protein scores, a cutoff for an Integrated error tolerant search and a threshold for calculating mudpit scores.

  • A value of 0 indicates no cutoff - report maxHitsToReport 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. This value is also used to select proteins for an Integrated error tolerant search.
  • 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.
  • 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.

Other points to note:

  • 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, unless the ms_mascotresults::MSRES_MAXHITS_OVERRIDES_MINPROB flag is set. With versions of parser before Mascot 2.2, this flag was not available so AUTO in the standard Mascot results reports was implemented by setting this probablility to a (user) defined value and setting maxHitsToReport to a very large number.
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.

Returns:
The single hit parameter value if available.
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 ms_mascotresfile::get_ms_mascotresults_params(const ms_mascotoptions & opts, ms_mascotresults_params & 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.
void setFlags ( const unsigned int  flags )

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

Parameters:
flagsShould 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:
flags2Should 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:
ignoreIonsScoreBelowis 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.
void setMaxHitsToReport ( const int  maxHitsToReport )

Sets the maximum number of protein hits to report.

Parameters:
maxHitsToReportis 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.
void setMinPepLenInPeptideSummary ( const int  minPepLenInPeptideSummary )

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

Parameters:
minPepLenInPeptideSummaryis 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 probabilty cutoff point for protein scores, a cutoff for an Integrated error tolerant search and a threshold for calculating mudpit scores.

Parameters:
minProbabilityspecifies a cutoff point for protein scores, a cutoff for an Integrated error tolerant search and a threshold for calculating MudPIT scores.

  • A value of 0 indicates no cutoff - report maxHitsToReport 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. This value is also used to select proteins for an Integrated error tolerant search.
  • 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.
  • 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.

Other points to note:

  • 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, unless the ms_mascotresults::MSRES_MAXHITS_OVERRIDES_MINPROB flag is set. With versions of parser before Mascot 2.2, this flag was not available so AUTO in the standard Mascot results reports was implemented by setting this probablility to a (user) defined value and setting maxHitsToReport to a very large number.
void setSingleHit ( const char *  singleHit )

Sets the optional single hit parameter.

Parameters:
singleHitshould 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 setUnigeneIndexFile ( const char *  unigeneIndexFile )

Sets the optional file path to a UniGene Index file.

Parameters:
unigeneIndexFileis 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 ms_mascotresfile::get_ms_mascotresults_params(const ms_mascotoptions & opts, ms_mascotresults_params & 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:
usePeptideSummaryPass in true if the result file contains MS/MS data, false if not

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