23#ifndef _SERIALIZER_PEPXML_HPP_
24#define _SERIALIZER_PEPXML_HPP_
45 Config(
bool readSpectrumQueries =
true) : readSpectrumQueries(readSpectrumQueries) {}
51 void write(std::ostream& os,
const IdentData& mzid,
const std::string& filepath,
67 std::string
cut, no_cut, sense;
MZIDData <-> pepXML stream serialization.
Serializer_pepXML(const Config &config=Config())
void read(boost::shared_ptr< std::istream > is, IdentData &mzid, const pwiz::util::IterationListenerRegistry *=0) const
read in MZIDData object from a pepXML istream
Serializer_pepXML(Serializer_pepXML &)
Serializer_pepXML & operator=(Serializer_pepXML &)
void write(std::ostream &os, const IdentData &mzid, const std::string &filepath, const pwiz::util::IterationListenerRegistry *=0) const
write MZIDData object to ostream as pepXML
handles registration of IterationListeners and broadcast of update messages
PWIZ_API_DECL PepXMLSpecificity pepXMLSpecificity(const Enzyme &ez)
converts an identdata::Enzyme into a pepXML cut/no_cut/sense tuple
PWIZ_API_DECL CVID nativeIdStringToCVID(const std::string &id)
attempts to convert a period-delimited id into a nativeID format (e.g. "1.0.123" appears to be a Ther...
PWIZ_API_DECL const std::string & softwareCVIDToPepXMLSoftwareName(CVID softwareCVID)
converts a software CVID to the preferred name for that software in pepXML; an unrecognized software ...
PWIZ_API_DECL std::string stripChargeFromConventionalSpectrumId(const std::string &id)
strips charge state from known conventions of the pepXML spectrum attribute; used to find a unique id...
PWIZ_API_DECL CVID pepXMLScoreNameToCVID(CVID softwareCVID, const std::string &scoreName)
for a given software CVID, converts a pepXML score name into its corresponding CVID,...
PWIZ_API_DECL const std::string & scoreCVIDToPepXMLScoreName(CVID softwareCVID, CVID scoreCVID)
for a given software CVID, converts a score CVID into the preferred name for that score in pepXML; an...
PWIZ_API_DECL CVID pepXMLSoftwareNameToCVID(const std::string &softwareName)
converts a software name stored in pepXML software element into its corresponding CVID,...
Implementation of EnzymeType from the mzIdentML schema.
Implementation of the MzIdentMLType from the mzIdentML schema.
Serializer_pepXML configuration.
Config(bool readSpectrumQueries=true)