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