MultiplexFiltering.h File Reference

#include <OpenMS/KERNEL/BaseFeature.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/PROCESSING/CENTROIDING/PeakPickerHiRes.h>
#include <OpenMS/FEATUREFINDER/MultiplexIsotopicPeakPattern.h>
#include <OpenMS/FEATUREFINDER/MultiplexFilteredMSExperiment.h>
#include <OpenMS/FEATUREFINDER/MultiplexFilteredPeak.h>
#include <OpenMS/MATH/MISC/CubicSpline2d.h>
#include <functional>
#include <optional>
#include <vector>
#include <algorithm>
#include <iostream>

Go to the source code of this file.

Classes
class	MultiplexFiltering
	base class for filtering centroided and profile data for peak patterns More...
struct	MultiplexFiltering::BlacklistWriter
	a filtered peak that blacklisted a peak, and the mass trace of its pattern it reserved the peak for More...
struct	MultiplexFiltering::BlacklistOwner
	who blacklisted a peak: the first and the last filtered peak that reserved it (the same if only one did) More...
struct	MultiplexFiltering::BlacklistEntry
	an entry of blacklist_ (spectrum index and peak index in exp_centroided_) and a value read from or written to it More...
struct	MultiplexFiltering::BlacklistOwnerRecord
	the owners of a peak of blacklist_ that more than one filtered peak reserved (indices in filtered_peaks_) More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::MultiplexFiltering::BlacklistWriter

struct OpenMS::MultiplexFiltering::BlacklistWriter

a filtered peak that blacklisted a peak, and the mass trace of its pattern it reserved the peak for

Class Members
int	mass_trace	mass trace of the pattern the peak was reserved for (peptide * isotopes_per_peptide_max + isotope)
unsigned	pattern_idx	index of the pattern, i.e. of its filter result in the list filter() returns
unsigned	peak_idx	index of the filtered peak in the filter result of the pattern (MultiplexFilteredMSExperiment::getPeak()); it fits in an int, since the filtered peaks of all patterns together are limited to INT_MAX (see applyBlacklistEntries_())

OpenMS::MultiplexFiltering::BlacklistOwner

struct OpenMS::MultiplexFiltering::BlacklistOwner

who blacklisted a peak: the first and the last filtered peak that reserved it (the same if only one did)

Class Members
BlacklistWriter	first	the first filtered peak that reserved the peak
BlacklistWriter	last	the last one, whose mass trace the blacklist holds

OpenMS::MultiplexFiltering::BlacklistEntry

struct OpenMS::MultiplexFiltering::BlacklistEntry

an entry of blacklist_ (spectrum index and peak index in exp_centroided_) and a value read from or written to it

Class Members
size_t	mz_idx
size_t	rt_idx
int	value

OpenMS::MultiplexFiltering::BlacklistOwnerRecord

struct OpenMS::MultiplexFiltering::BlacklistOwnerRecord

the owners of a peak of blacklist_ that more than one filtered peak reserved (indices in filtered_peaks_)

Class Members
int	first	the first filtered peak that reserved the peak
int	first_value	the value first left in blacklist_ (read when another filtered peak reserved the peak for the first time)
int	last	the last filtered peak that reserved the peak, whose value blacklist_ holds