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23 #ifndef _PEAKDATA_HPP_
24 #define _PEAKDATA_HPP_
33 #include "boost/shared_ptr.hpp"
45 using namespace minimxml::SAXParser;
63 std::vector<pwiz::math::OrderedPair>
data;
77 Peak(
double _mz = 0,
double _retentionTime = 0);
85 void read(std::istream& is);
94 parseCharacters =
true;
95 autoUnescapeCharacters =
false;
144 Scan() : index(0), scanNumber(0), retentionTime(0), observationDuration(0) {}
181 Software() : name(
""), version(
""), source(
""), parameters(0) {}
332 #endif // _PEAKDATA_HPP_
FeatureFile(FeatureFile &)
bool operator==(const Parameter &that) const
std::vector< pwiz::math::OrderedPair > data
void write(minimxml::XMLWriter &xmlWriter) const
The XMLWriter class provides simple, tag-level XML syntax writing.
const int PeakDataFormatVersion_Major
bool operator!=(const PeakFamily &that) const
double retentionTimeMin() const
void write(pwiz::minimxml::XMLWriter &xmlWriter) const
boost::shared_ptr< Feature > FeaturePtr
HandlerPeakel _handlerPeakel
SAX event handler interface.
virtual Status startElement(const std::string &name, const Attributes &attributes, stream_offset position)
double sumAmplitude() const
bool operator==(const Software &that) const
void write(minimxml::XMLWriter &writer) const
bool operator==(const PeakFamily &that) const
std::vector< Parameter > parameters
double retentionTimeMax() const
double observationDuration
Peak(double _mz=0, double _retentionTime=0)
bool operator==(const Scan &scan) const
double retentionTimeMax() const
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
void read(std::istream &is)
struct for an eluted peak (PEAK ELution)
PWIZ_API_DECL std::istream & operator>>(std::istream &is, Peak &peak)
void write(minimxml::XMLWriter &xmlWriter) const
virtual Status characters(const SAXParser::saxstring &text, stream_offset position)
void read(std::istream &is)
bool operator!=(const Peakel &that) const
bool operator!=(const Scan &scan) const
std::vector< Peak > peaks
void read(std::istream &is)
HandlerPeak(Peak *_peak=0)
bool operator==(const Peakel &that) const
std::vector< FeaturePtr > features
Handler returns the Status struct as a means of changing the parser's behavior.
boost::shared_ptr< Peakel > PeakelPtr
void calculateMetadata()
recalculates all metadata based on peak data
void write(pwiz::minimxml::XMLWriter &xmlWriter) const
bool operator!=(const Peak &that) const
FeatureFile operator=(FeatureFile &)
bool operator!=(const Software &that) const
virtual Status startElement(const std::string &name, const Attributes &attributes, stream_offset position)
bool operator!=(const PeakData &that) const
void read(std::istream &is)
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...
std::vector< PeakFamily > peakFamilies
void write(minimxml::XMLWriter &writer) const
PWIZ_API_DECL const Record & record(Type type)
returns the amino acid's Record by type
Parameter(std::string name_, std::string value_)
void read(std::istream &is)
void write(minimxml::XMLWriter &writer) const
void read(std::istream &is)
double retentionTimeMin() const
double getAttribute(Attribute attribute) const
void read(std::istream &is)
CalibrationParameters calibrationParameters
bool operator==(const PeakData &that) const
PWIZ_API_DECL std::ostream & operator<<(std::ostream &os, const Peak &peak)
void write(pwiz::minimxml::XMLWriter &xmlWriter) const
bool operator!=(const Feature &that) const
std::vector< Peak > peaks
bool operator==(const Peak &that) const
std::vector< PeakelPtr > peakels
HandlerFeature(Feature *_feature=0)
bool operator==(const Feature &that) const
std::vector< Scan > scans
std::map< Attribute, double > Attributes
virtual Status startElement(const std::string &name, const Attributes &attributes, stream_offset position)
const int PeakDataFormatVersion_Minor
boost::iostreams::stream_offset stream_offset
std::string sourceFilename
HandlerPeakel(Peakel *_peakel=0)
void read(std::istream &is)
void read(std::istream &is)
void write(pwiz::minimxml::XMLWriter &xmlWriter) const
Feature(const MSIHandler::Record &record)
bool operator!=(const Parameter &that) const