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24 #ifndef _PEAKDETECTORMATCHEDFILTER_HPP_
25 #define _PEAKDETECTORMATCHEDFILTER_HPP_
88 : isotopeEnvelopeEstimator(0),
90 filterSampleRadius(0),
91 peakThresholdFactor(0),
92 peakMaxCorrelationAngle(0),
93 isotopeThresholdFactor(0),
94 monoisotopicPeakThresholdFactor(0),
95 isotopeMaxChargeState(0),
96 isotopeMaxNeutronCount(0),
98 useMagnitudeFilter(false),
109 static std::auto_ptr<PeakDetectorMatchedFilter>
create(
const Config& config);
140 std::vector<pwiz::data::peakdata::Peak>
peaks;
142 Score(
double _f = 0,
int _c = 0,
int _n = 0)
143 : frequency(_f), charge(_c), neutronCount(_n),
144 value(0), monoisotopicFrequency(0), monoisotopicIntensity(0),
152 std::vector<Score>& scores)
const = 0;
165 #endif // _PEAKDETECTORMATCHEDFILTER_HPP_
std::vector< pwiz::data::peakdata::Peak > peaks
std::complex< double > monoisotopicIntensity
std::ostream * log
log stream (0 == no logging)
Score(double _f=0, int _c=0, int _n=0)
virtual void findPeaks(const pwiz::data::FrequencyData &fd, pwiz::data::peakdata::Scan &result) const =0
Find the peaks in the frequency data, filling in Scan structure.
double collapseRadius
multiple peaks within this radius (Hz) are reported as single peak
MatchedFilter implementation of the PeakDetector interface.
virtual void findPeaks(const pwiz::data::FrequencyData &fd, pwiz::data::peakdata::Scan &result, std::vector< Score > &scores) const =0
same as PeakDetector::findPeaks(), but provides additional Score information
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
int isotopeMaxChargeState
isotope filter maximum charge state to score
Class for binary storage of complex frequency data.
int logDetailLevel
log detail level (0 == normal, 1 == extra)
Class used for calculating a theoretical isotope envelope for a given mass, based on an estimate of t...
int isotopeMaxNeutronCount
isotope filter maximum number of neutrons to score
double peakMaxCorrelationAngle
maximum correlation angle (degrees) for initial peak reporting
double peakThresholdFactor
noise floor multiple for initial peak reporting threshold
int filterMatchRate
number of filter correlations computed per frequency step
int filterSampleRadius
number of filter samples taken on either side of 0
static std::auto_ptr< PeakDetectorMatchedFilter > create(const Config &config)
create an instance.
virtual const Config & config() const =0
access to the configuration
virtual ~PeakDetectorMatchedFilter()
double monoisotopicFrequency
PWIZ_API_DECL std::ostream & operator<<(std::ostream &os, const PeakDetectorMatchedFilter::Score &a)
structure for holding the matched filter calculation results
const chemistry::IsotopeEnvelopeEstimator * isotopeEnvelopeEstimator
IsotopeEnvelopeEstimator pointer, must be valid for PeakDetector lifetime.
bool useMagnitudeFilter
use the magnitude of the peak shape filter kernel for finding peaks
double monoisotopicPeakThresholdFactor
noise floor multiple for monoisotopic peak threshold
Interface for finding peaks in frequency data.
double isotopeThresholdFactor
noise floor multiple for isotope filter threshold
structure for holding configuration