FragmentIndex.h File Reference

#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/Peak1D.h>
#include <array>
#include <mutex>
#include <vector>
#include <functional>
#include <algorithm>

Go to the source code of this file.

Classes
class	FragmentIndex
	Generates from a set of Fasta files a 2D-datastructure which stores all theoretical masses of all b and y ions from all peptides generated from the Fasta file. The datastructure is build such that on one axis the fragments are sorted by their own mass and the axis by the mass of their precursor/protein. The FI has two options: Bottom-up and Top Down. In later digestion is skiped and the fragments have a direct reference to the mass of the proteins instead of digested peptides. More...
struct	FragmentIndex::Peptide
	Compact descriptor of a peptide instance held by the FragmentIndex. More...
struct	FragmentIndex::Peptide::Span
struct	FragmentIndex::SpectrumMatch
	Match between a query peak and an entry in the DB. More...
struct	FragmentIndex::SpectrumMatchesTopN
	container for SpectrumMatch. Also keeps count of total number of candidates and total number of matches. More...
struct	FragmentIndex::RemovedOccurrence
	A protein occurrence of an indexed peptidoform that peptide:deduplicate removed from the index. More...
struct	FragmentIndex::Hit
struct	FragmentIndex::Fragment
	One entry in the fragment index. More...
struct	FragmentIndex::PeptidoformRendering_
	Rendering classes of the configured modifications, for samePeptidoform_() (peptide:deduplicate) More...
struct	FragmentIndex::VarModEntry
	Entry in the per-AA variable modification lookup table. More...
struct	FragmentIndex::ModSlot
	A candidate modification slot for a specific peptide. More...
struct	FragmentIndex::ModShift_
struct	FragmentIndex::IonOffsets
	Precomputed ion-type mass offsets (from Residue::getInternalTo*Ion formulas) More...
struct	FragmentIndex::CandidateBlock_
	One (precursor charge, isotope error) block of a queryPeaks() call. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::FragmentIndex::SpectrumMatch

struct OpenMS::FragmentIndex::SpectrumMatch

Match between a query peak and an entry in the DB.

Class Members
int16_t	isotope_error_ {}	The isotope_error used for the performed search.
uint32_t	num_matched_ {}	Number of peaks-fragment hits.
size_t	peptide_idx_ {}	The idx this struct belongs to.
uint16_t	precursor_charge_ {}	The precursor_charge used for the performed search.
uint16_t	realized_length_ {}	Peptide-mass mode: length of the realized sub-peptide, a prefix of the mother peptide_idx_. 0 without low_memory.
float	sigma_delta_ {}	Peptide-mass mode: Σ of the variable-mod deltas of subset_bitmask_. 0 without low_memory or unmodified.
uint32_t	subset_bitmask_ {}	Peptide-mass mode: active slots in the slot list returned by buildModSlots_ for the realized sub-peptide. 0 = unmodified. Ignored without low_memory.

OpenMS::FragmentIndex::RemovedOccurrence

struct OpenMS::FragmentIndex::RemovedOccurrence

A protein occurrence of an indexed peptidoform that peptide:deduplicate removed from the index.

The removed entry had the same peptidoform (reconstructModifiedSequence(...).toString()) as the kept entry getPeptides()[peptide_idx], hence the same length; it started at start in protein protein_idx.

Class Members
UInt32	peptide_idx	index into getPeptides() of the kept entry of the same peptidoform
UInt32	protein_idx	protein of the removed entry (index into the FASTA entries passed to build())
uint16_t	start	0-based start of the removed entry in that protein

OpenMS::FragmentIndex::VarModEntry

struct OpenMS::FragmentIndex::VarModEntry

Entry in the per-AA variable modification lookup table.

Class Members
double	delta_mass	mass delta from this modification
const ResidueModification *	mod_ptr	pointer to the modification (for AASequence reconstruction)
TermSpecificity	term_spec	where this mod can be applied

OpenMS::FragmentIndex::ModShift_

struct OpenMS::FragmentIndex::ModShift_

Peptide-mass mode: a shift Σ at which querySpectrumPeptideMasses_() looks up prefixes. A peptidoform belongs to the shift closest to the sum of its modification deltas.

Class Members
size_t	min_mods	the fewest variable modifications that sum to it (within the matching tolerance)
bool	protein_terminal	only reached with a protein-terminal modification: the prefix must start or end a protein
double	sigma	the shift

OpenMS::FragmentIndex::IonOffsets

struct OpenMS::FragmentIndex::IonOffsets

Precomputed ion-type mass offsets (from Residue::getInternalTo*Ion formulas)

Class Members
double	a_offset {0.0}
double	b_offset {0.0}
double	c_offset {0.0}
double	x_offset {0.0}
double	y_offset {0.0}
double	z_offset {0.0}
double	zp1_offset {0.0}	z+1 (z-dot) ions, the main C-terminal fragments of ETD-type spectra

OpenMS::FragmentIndex::CandidateBlock_

struct OpenMS::FragmentIndex::CandidateBlock_

One (precursor charge, isotope error) block of a queryPeaks() call.

Class Members
size_t	cell_offset	sum of the range sizes of the preceding blocks of the call
size_t	first	half-open range [first, second) of peptides the precursor could belong to
int16_t	isotope_error	the applied isotope error
size_t	second