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Matrix Science Mascot Parser toolkit
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Matrix Science Mascot Parser toolkit
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The details of a Distiller search. More...
#include <ms_distiller_data_search.hpp>
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, bool isTargetFDR=false, const std::string &targetFDRType="", const std::string &targetFDRStr="") | |
| 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. | |
| ms_mascotresults::DECOY_STATS_COUNT_TYPE | getFDRCountType () const |
| Returns the value of getTargetFDRType() transposed to the ms_mascotresults::DECOY_STATS_COUNT_TYPE enum. | |
| 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. | |
| double | getTargetFDR () const |
| Returns the numeric target fdr. | |
| std::string | getTargetFDRStr () const |
| Returns the encoded target fdr for the targetFDR attribute. | |
| std::string | getTargetFDRType () const |
| Returns the fdrType option for the targetFDR attribute. | |
| std::string | getTaskId () const |
| The task ID of the Mascot search. | |
| bool | isTargetFDR () const |
| Returns the "use" option for the targetFDR attribute. | |
| bool | serverVersionNewerOrSameAs (int major, int minor, int patch) const |
| Compare the version of the Mascot Server with the specified values. | |
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
| enum eGrouping |
Setting to control how proteins are grouped.
See Using enumerated values and static const ints in Perl, Java, Python and C#.
| 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. |
| 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, | ||
| bool | isTargetFDR = false, |
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| const std::string & | targetFDRType = "", |
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| const std::string & | targetFDRStr = "" |
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| ) |
Constructor with all values.
| 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> |
| isTargetFDR | comes from the "use" attribute in the <targetFDR> [default=false] |
| targetFDRType | comes from the "fdrType" attribute in the <targetFDR> [default=empty string] |
| targetFDRStr | comes from the "targetFDRStr" attribute in the <targetFDR> [default=empty string] |
| 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.
| 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.
| ms_mascotresults::DECOY_STATS_COUNT_TYPE getFDRCountType | ( | ) | const |
Returns the value of getTargetFDRType() transposed to the ms_mascotresults::DECOY_STATS_COUNT_TYPE enum.
Default value ms_mascotresults::DECOY_STATS_COUNT_TYPE::DS_COUNT_PSM
| 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.
| 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.
| 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
| resultsFilePath | is, for example: "../data/2018010/F0012345.dat" |
| 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
| 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_mascotresfilebase::get_ms_mascotresults_params but we don't have a ms_mascotresfilebase object available.
| 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.
| bool getPercolator | ( | ) | const |
Return true if the percolator is in use.
Default value: false
Obtained from the percolator attribute in the <blueoptions> element.
| 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
| 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
| 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.
| 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().
| 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.
| bool getRequireBoldRed | ( | ) | const |
Return true if bold, red font should be used.
Default value: false
Obtained from the requireBoldRed attribute in the <blueoptions> element.
| double getScoreExpectCutOff | ( | ) | const |
Return the score cutoff threshold value.
Default value: 0
Obtained from the ScoreExpectCutOff attribute in the <blueoptions> element.
| 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.
| 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.
| 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.
| 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.
| bool getShowSubsetFamily | ( | ) | const |
Return true if family subsets should be shown.
Default value: false
Obtained from the showSubsetFamily attribute in the <blueoptions> element.
| 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.
| 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".
| double getTargetFDR | ( | ) | const |
Returns the numeric target fdr.
Default value 0: Obtained from the targetFDRStr attribute in <targetFDR> element
| std::string getTargetFDRStr | ( | ) | const |
Returns the encoded target fdr for the targetFDR attribute.
Default value: empty string Obtained from the targetFDRStr attribute in <targetFDR> element The Base64 encoded target FDR
| std::string getTargetFDRType | ( | ) | const |
Returns the fdrType option for the targetFDR attribute.
Default value: empty string Obtained from the fdrType attribute in <targetFDR> element Should be one of either "psm" or "sequence" if set
| std::string getTaskId | ( | ) | const |
The task ID of the Mascot search.
Default value: empty string
Obtained from the TaskID attribute in the <MascotSearch> element.
| bool isTargetFDR | ( | ) | const |
Returns the "use" option for the targetFDR attribute.
Default value: false Obtained from the use attribute in <targetFDR> element
| bool serverVersionNewerOrSameAs | ( | int | major, |
| int | minor, | ||
| int | patch | ||
| ) | const |
Compare the version of the Mascot Server with the specified values.
| 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 |
1.9.6