33#include "boost/shared_ptr.hpp"
45using namespace minimxml::SAXParser;
63 std::vector<pwiz::math::OrderedPair>
data;
77 Peak(
double _mz = 0,
double _retentionTime = 0);
85 void read(std::istream& is);
144 Scan() : index(0), scanNumber(0), retentionTime(0), observationDuration(0) {}
171 Parameter(std::string name_, std::string value_) : name(name_), value(value_) {}
181 Software() : name(
""), version(
""), source(
""), parameters(0) {}
SAX event handler interface.
bool parseCharacters
When false, no calls to characters() will be made.
bool autoUnescapeCharacters
boost::iostreams::stream_offset stream_offset
The XMLWriter class provides simple, tag-level XML syntax writing.
const int PeakDataFormatVersion_Minor
boost::shared_ptr< Feature > FeaturePtr
const int PeakDataFormatVersion_Major
PWIZ_API_DECL std::ostream & operator<<(std::ostream &os, const Peak &peak)
boost::shared_ptr< Peakel > PeakelPtr
PWIZ_API_DECL std::istream & operator>>(std::istream &is, Peak &peak)
std::vector< FeaturePtr > features
void write(pwiz::minimxml::XMLWriter &xmlWriter) const
void read(std::istream &is)
FeatureFile(FeatureFile &)
FeatureFile operator=(FeatureFile &)
bool operator==(const Feature &that) const
void read(std::istream &is)
std::vector< PeakelPtr > peakels
double retentionTimeMax() const
Feature(const MSIHandler::Record &record)
double retentionTimeMin() const
bool operator!=(const Feature &that) const
void write(pwiz::minimxml::XMLWriter &xmlWriter) const
HandlerFeature(Feature *_feature=0)
HandlerPeakel _handlerPeakel
virtual Status startElement(const std::string &name, const Attributes &attributes, stream_offset position)
HandlerPeak(Peak *_peak=0)
virtual Status characters(const SAXParser::saxstring &text, stream_offset position)
virtual Status startElement(const std::string &name, const Attributes &attributes, stream_offset position)
HandlerPeakel(Peakel *_peakel=0)
virtual Status startElement(const std::string &name, const Attributes &attributes, stream_offset position)
std::vector< Scan > scans
void write(pwiz::minimxml::XMLWriter &xmlWriter) const
void read(std::istream &is)
std::string sourceFilename
bool operator!=(const PeakData &that) const
bool operator==(const PeakData &that) const
void write(minimxml::XMLWriter &writer) const
bool operator==(const PeakFamily &that) const
bool operator!=(const PeakFamily &that) const
void read(std::istream &is)
double sumAmplitude() const
std::vector< Peak > peaks
Peak(double _mz=0, double _retentionTime=0)
std::map< Attribute, double > Attributes
void write(minimxml::XMLWriter &writer) const
double getAttribute(Attribute attribute) const
bool operator!=(const Peak &that) const
void read(std::istream &is)
std::vector< pwiz::math::OrderedPair > data
bool operator==(const Peak &that) const
struct for an eluted peak (PEAK ELution)
void calculateMetadata()
recalculates all metadata based on peak data
void read(std::istream &is)
bool operator!=(const Peakel &that) const
bool operator==(const Peakel &that) const
double retentionTimeMin() const
std::vector< Peak > peaks
double retentionTimeMax() const
void write(pwiz::minimxml::XMLWriter &xmlWriter) const
CalibrationParameters calibrationParameters
std::vector< PeakFamily > peakFamilies
bool operator!=(const Scan &scan) const
void write(minimxml::XMLWriter &writer) const
double observationDuration
bool operator==(const Scan &scan) const
void read(std::istream &is)
void read(std::istream &is)
bool operator!=(const Parameter &that) const
Parameter(std::string name_, std::string value_)
bool operator==(const Parameter &that) const
void write(minimxml::XMLWriter &xmlWriter) const
std::vector< Parameter > parameters
void write(minimxml::XMLWriter &xmlWriter) const
bool operator!=(const Software &that) const
bool operator==(const Software &that) const
void read(std::istream &is)
Handler returns the Status struct as a means of changing the parser's behavior.