24 #ifndef _MINIMUMPEPXML_HPP_ 25 #define _MINIMUMPEPXML_HPP_ 29 #include "boost/shared_ptr.hpp" 30 #include "boost/logic/tribool.hpp" 69 void read(std::istream& is);
105 void read(std::istream& is);
124 void read(std::istream& is);
133 Q3RatioResult() : lightFirstScan(0), lightLastScan(0), lightMass(0), heavyFirstScan(0), heavyLastScan(0), heavyMass(0), lightArea(0), heavyArea(0), q2LightArea(0), q2HeavyArea(0), decimalRatio(0) {}
148 void read(std::istream& is);
225 void read(std::istream& is);
241 void read(std::istream& is);
257 void read(std::istream& is);
272 void read(std::istream& is);
287 void read(std::istream& is);
304 void read(std::istream& is);
320 void read(std::istream& is);
329 SearchHit() : hitRank(0),numTotalProteins(0), numMatchedIons(0), totalNumIons(0), calcNeutralPepMass(0), massDiff(0), numTolTerm(0), numMissedCleavages(0), isRejected(0) {}
352 void read(std::istream& is);
374 void read(std::istream& is);
395 void read(std::istream& is);
416 void read(std::istream& is);
457 void read(std::istream& is);
489 SpectrumQuery() : startScan(0), endScan(0), precursorNeutralMass(0), assumedCharge(0), index(0), retentionTimeSec(0) {}
513 void read(std::istream& is);
542 void read(std::istream& is);
637 void read(std::istream& is);
647 Match(
const SpectrumQuery& _spectrumQuery,
FeaturePtr _feature,
double _score = 0) : score(_score), spectrumQuery(_spectrumQuery), feature(_feature) {}
657 void read(std::istream& is);
676 MatchData(std::string wfc, std::string snc) : warpFunctionCalculator(wfc), searchNbhdCalculator(snc) {}
677 MatchData(std::vector<MatchPtr> _matches) : matches(_matches){}
684 void read(std::istream& is);
697 #endif // _MINIMUMPEPXML_HPP_
std::string searchEngine
SEQUEST, Mascot, COMET, etc.
int index
Search constraint applied specifically to this query.
std::vector< std::string > inputFile
boost::shared_ptr< Match > MatchPtr
EnzymaticSearchConstraint enzymaticSearchConstraint
Match(const SpectrumQuery &_spectrumQuery, FeaturePtr _feature, double _score=0)
The XMLWriter class provides simple, tag-level XML syntax writing.
std::string fidelity
Semispecific means that at least one end of a pepide must conform to the cleavage specificity...
SpectrumQuery spectrumQuery
std::string peptideNextAA
int startScan
first scan number integrated into MS/MS spectrum
size_t searchId
Unique identifier to search summary.
std::string msManufacturer
Manufacturer of MS/MS instrument.
Parameter(const std::string &name="", const std::string &value="")
std::vector< DataFilterPtr > dataFilters
std::string precursorMassType
average or monoisotopic
std::vector< SearchScorePtr > searchScore
std::vector< SearchResultPtr > searchResult
Reference for analysis applied to current run (time corresponds with analysis_summary/, id corresponds with analysis_result/)
std::string sense
Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut ...
std::string peptideTerminus
AnalysisResult analysisResult
std::string noCut
Zero or more 1-letter residue codes.
void setLogStream(std::ostream &os)
std::string peptidePrevAA
std::string searchNbhdCalculator
std::string raw_data
raw data type extension (e.g. .mzXML)
boost::shared_ptr< AnalysisSummary > AnalysisSummaryPtr
std::vector< AminoAcidModification > aminoAcidModifications
double retentionTimeSec
Unique identifier.
std::string raw_data_type
raw data type extension (e.g. .mzXML)
std::string msDetector
EMT, etc(cf mzXML)
double calcNeutralPepMass
std::vector< SearchSummaryPtr > searchSummary
int assumedCharge
Precursor ion charge used for search.
std::string searchID
Format of file storing the runner up peptides (if not present in pepXML)
PWIZ_API_DECL bool operator==(const MatchPtr left, const MatchPtr right)
boost::shared_ptr< SearchScore > SearchScorePtr
std::vector< AlternativeProtein > alternativeProteins
ModAminoAcidMass modAminoAcidMass
size_t minSpace
minimum separation between adjacent cleavages. default 1.
boost::shared_ptr< SearchResult > SearchResultPtr
std::vector< SearchHitPtr > searchHit
boost::shared_ptr< SearchSummary > SearchSummaryPtr
boost::shared_ptr< SearchHit > SearchHitPtr
std::string parent_file
File from which derived.
std::vector< PeptideProphetSummary > peptideprophet_summary
std::string fragmentMassType
average or monoisotopic
std::string XSISchemaLocation
boost::shared_ptr< Feature > FeaturePtr
std::string time
Date of analysis.
Database search settings.
std::string raw_data_type
std::string baseName
full path file name of mzXML (minus the .mzXML)
SearchResult(size_t searchId=0)
std::string cut
One or more 1-letter residue codes.
std::string databaseReleaseIdentifier
PeptideProphetResult peptideProphetResult
MSMSRunSummary msmsRunSummary
std::vector< RocDataPoint > roc_data_point
std::string version
Release.
std::string modifiedPeptide
boost::shared_ptr< DataFilter > DataFilterPtr
std::vector< double > allNttProb
MatchData(std::vector< MatchPtr > _matches)
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
Source and filtering criteria used to generate dataset.
SearchScore(const std::string &name="", const std::string &value="")
std::string baseName
Full path location of mzXML file for this search run (without the .mzXML extension) ...
std::string msManufacturer
std::string msIonization
Instrument model (cf mzXML)
size_t id
Unique identifier for each type of analysis.
std::string name
Controlled code name for the enzyme that can be referred to by applications.
double est_tot_num_correct
std::vector< DistributionPoint > distribution_point
double probability(const vector< double > &p, const vector< int > &i)
std::vector< MatchPtr > matches
std::string analysis
Name of analysis program.
std::string msMassAnalyzer
long precursor_ion_charge
SearchDatabase searchDatabase
runner up search hit data type extension (e.g. .tgz)
std::string warpFunctionCalculator
ModificationInfo modificationInfo
std::vector< SpectrumQueryPtr > spectrumQueries
PWIZ_API_DECL void read(std::istream &is, CV &cv)
Q3RatioResult q3RatioResult
std::string msModel
Instrument model (cf mzXML)
PWIZ_API_DECL Position position(CVID cvid=CVID_Unknown)
returns a Position corresponding to one of the following CVIDs: CVID_Unknown: Position::Anywhere MS_m...
size_t search_id
matches id in search hit
std::vector< ParameterPtr > parameters
MatchData(std::string wfc, std::string snc)
std::vector< MixtureModel > mixture_model
AnalysisSummaryPtr analysisSummary
int endScan
last scan number integrated into MS/MS spectrum
boost::tribool independent
If there are multiple specificities and independent is true, then a single peptide cannot exhibit one...
boost::shared_ptr< DatasetDerivation > DatasetDerivationPtr
double precursorNeutralMass
std::string msMassAnalyzer
Ion trap, etc (cf mzXML)
boost::shared_ptr< SpectrumQuery > SpectrumQueryPtr
std::string description
Free text to describe alternative names, special conditions, etc.
std::vector< ErrorPoint > error_point
EnzymaticSearchConstraint()
PWIZ_API_DECL std::string value(const std::string &id, const std::string &name)
convenience function to extract a named value from an id string
std::string time
Time analysis complete (unique id)
PWIZ_API_DECL bool operator!=(const TruncatedLorentzianParameters &t, const TruncatedLorentzianParameters &u)
DatasetDerivationPtr datasetDerivation
std::string description
filtering criteria applied to data
int maxNumInternalCleavages
std::string windows_parent
std::string analsysis
Analysis name.
boost::shared_ptr< Parameter > ParameterPtr
size_t generation_no
number preceding filter generations
SampleEnzyme sampleEnzyme