NuXLIonLikelihood.h File Reference

#include <OpenMS/ANALYSIS/ID/FragmentIonLikelihoodModel.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <array>
#include <cstdint>
#include <vector>

Go to the source code of this file.

Classes
class	NuXLIonLikelihood
	Self-trained fragment ion likelihood for protein-nucleic acid cross-links (after ProSE's ion priors). More...
struct	NuXLIonLikelihood::Outcomes
	Matched ions of one hypothesis (hit or its reversed sequence) More...
struct	NuXLIonLikelihood::Evidence
	Matched ions of a hit and of its noise hypothesis. More...
struct	NuXLIonLikelihood::Features
	Features of one hit. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::NuXLIonLikelihood::Outcomes

struct OpenMS::NuXLIonLikelihood::Outcomes

Matched ions of one hypothesis (hit or its reversed sequence)

Class Members
vector< uint8_t >	groups	Group of each ion.
vector< Ion >	ions

OpenMS::NuXLIonLikelihood::Evidence

struct OpenMS::NuXLIonLikelihood::Evidence

Matched ions of a hit and of its noise hypothesis.

Class Members
Outcomes	noise	empty if the reversed sequence equals the sequence
Outcomes	signal

OpenMS::NuXLIonLikelihood::Features

struct OpenMS::NuXLIonLikelihood::Features

Features of one hit.

Class Members
double	explained_presence = 0.0	sum of P(present) of the matched ions / sum over all ions
double	llr = 0.0	summed log-likelihood ratio of all ions
double	llr_shifted = 0.0	the part of llr from XL_SHIFTED and XL_UNLOCALIZED ions
double	top_predicted_observed = 0.0	fraction of the 6 ions with the highest P(present) that matched