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...

#include <OpenMS/ANALYSIS/ID/FragmentIndex.h>

Inheritance diagram for FragmentIndex:

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Collaboration diagram for FragmentIndex:

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Classes
struct	Fragment
	One entry in the fragment index. More...

struct	Hit

struct	IonOffsets
	Precomputed ion-type mass offsets (from Residue::getInternalTo*Ion formulas) More...

struct	ModSlot
	A candidate modification slot for a specific peptide. More...

struct	Peptide
	Compact descriptor of a peptide instance held by the FragmentIndex. More...

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

struct	SpectrumMatchesTopN
	container for SpectrumMatch. Also keeps count of total number of candidates and total number of matches. More...

struct	VarModEntry
	Entry in the per-AA variable modification lookup table. More...

Public Member Functions
	FragmentIndex ()
	Default constructor.

	~FragmentIndex () override=default
	Default destructor.

bool	isBuild () const
	Indicates whether the fragment index has been built.

const std::vector< Peptide > &	getPeptides () const
	Returns a reference to the internal peptide container.

void	build (const std::vector< FASTAFile::FASTAEntry > &fasta_entries)
	Given a set of Fasta files, builds the Fragment Index datastructure (FID). First all fragments are sorted by their own mass. Next they are placed in buckets. The min-fragment mass is stored for each bucket, whereupon the fragments are sorted within the buckets by their originating precursor mass.

void	clear ()
	Delete fragment index. Sets is_build=false.

std::pair< size_t, size_t >	getPeptidesInMassWindow (float precursor_mass, const std::pair< float, float > &window) const

std::vector< Hit >	query (const Peak1D &peak, const std::pair< size_t, size_t > &peptide_idx_range, uint16_t peak_charge)
	Queries one peak.

void	querySpectrum (const MSSpectrum &spectrum, SpectrumMatchesTopN &sms)
	: queries one complete experimental spectra against the Database. Loops over all precursor charges Starts at min_precursor_charge and iteratively goes to max_precursor_charge. We query all peaks multiple times with all the different precursor charges and corresponding precursor masses

AASequence	reconstructModifiedSequence (const Peptide &peptide, const std::vector< FASTAFile::FASTAEntry > &fasta_entries) const
	Reconstruct a fully modified AASequence from a Peptide's bitmask.

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages.

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.

virtual	~DefaultParamHandler ()
	Destructor.

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.

void	setParameters (const Param &param)
	Sets the parameters.

const Param &	getParameters () const
	Non-mutable access to the parameters.

const Param &	getDefaults () const
	Non-mutable access to the default parameters.

const String &	getName () const
	Non-mutable access to the name.

void	setName (const String &name)
	Mutable access to the name.

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections.

Static Public Member Functions
static bool	isOpenSearchMode (double lower_magnitude, double upper_magnitude, bool unit_ppm) noexcept

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values.

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method.

void	generatePeptides (const std::vector< FASTAFile::FASTAEntry > &fasta_entries)
	Generates all peptides from given fasta entries. If Bottom-up is set to false skips digestion. If set to true the Digestion enzyme can be set in the parameters. Additionally introduces fixed and variable modifications for restrictive PSM search.

void	initModificationTables_ ()

size_t	buildModSlots_ (const char sequence, size_t seq_len, ModSlot out_slots, bool is_protein_nterm=false, bool is_protein_cterm=false) const

void	generateFragmentsLightweight_ (std::vector< Fragment > &fragments, const char sequence, size_t seq_len, UInt32 peptide_idx, double n_term_mod_mass, double c_term_mod_mass, const double residue_mod_masses) const

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Static Protected Member Functions
static void	initResidueMassTable_ ()

Protected Attributes
bool	is_build_ {false}
	true, if the database has been populated with fragments

std::array< double, 128 >	fixed_mod_deltas_ {}
	Per-AA fixed modification delta mass (0.0 if no fixed mod applies)

std::array< const ResidueModification *, 128 >	fixed_mod_ptrs_ {}
	Per-AA fixed modification pointer (nullptr if none)

double	fixed_nterm_delta_ {0.0}
	Fixed N-terminal mod delta (0 if none)

double	fixed_cterm_delta_ {0.0}
	Fixed C-terminal mod delta (0 if none)

const ResidueModification *	fixed_nterm_mod_ptr_ {nullptr}

const ResidueModification *	fixed_cterm_mod_ptr_ {nullptr}

std::array< std::vector< VarModEntry >, 128 >	variable_mod_table_ {}
	Per-AA variable modification table: for each ASCII char, list of possible variable mods.

std::vector< VarModEntry >	variable_nterm_mods_
	Pure N-terminal variable mods (not residue-specific)

std::vector< VarModEntry >	variable_cterm_mods_
	Pure C-terminal variable mods (not residue-specific)

bool	mod_tables_initialized_ {false}

std::vector< Peptide >	fi_peptides_
	vector of all (digested) peptides

std::vector< Fragment >	fi_fragments_
	vector of all theoretical fragments (b- and y- ions)

float	fragment_min_mz_
	smallest fragment mz

float	fragment_max_mz_
	largest fragment mz

size_t	min_ion_index_ {0}
	skip ions below this index (0=all, 2=skip b1/b2/y1/y2)

size_t	bucketsize_
	number of fragments per outer node

std::vector< float >	bucket_min_mz_
	vector of the smalles fragment mz of each bucket

double	precursor_mass_tolerance_lower_ {20.0}
	positive magnitude, effective lower bound is -lower

double	precursor_mass_tolerance_upper_ {20.0}
	positive magnitude, effective upper bound is +upper

bool	precursor_mass_tolerance_unit_ppm_ {true}

float	fragment_mz_tolerance_

bool	fragment_mz_tolerance_unit_ppm_ {true}

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

String	error_name_
	Name that is displayed in error messages during the parameter checking.

bool	check_defaults_
	If this member is set to false no checking if parameters in done;.

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Static Protected Attributes
static constexpr size_t	MAX_MOD_SLOTS = 32
	max variable mod slots per peptide (uint32_t bitmask)

static std::array< double, 128 >	residue_mass_table_

static std::once_flag	mass_table_once_flag_

static IonOffsets	ion_offsets_

Private Member Functions
void	queryPeaks (SpectrumMatchesTopN &candidates, const MSSpectrum &spectrum, const std::pair< size_t, size_t > &candidates_range, const int16_t isotope_error, const uint16_t precursor_charge)
	queries peaks for a given experimental spectrum with a set range of potential peptides, isotope error and precursor charge. Hits are transferred into a PSM list. Technically an adapter between query(...) and openSearch(...)/searchDifferentPrecursorRanges(...)

void	searchDifferentPrecursorRanges (const MSSpectrum &spectrum, float precursor_mass, SpectrumMatchesTopN &sms, uint16_t charge)
	If closed search loops over all isotope errors. For each iteration loop over all peaks with queryPeaks.

void	trimHits (SpectrumMatchesTopN &init_hits) const
	places the k-largest elements in the front of the input array. Inside of the k-largest elements and outside the elements are not sorted

bool	isOpenSearchMode_ () const noexcept
	Instance delegate — same rule, reads the member bounds.

std::pair< float, float >	computeMassWindow_ (float precursor_mass) const

Private Attributes
bool	add_b_ions_

bool	add_y_ions_

bool	add_a_ions_

bool	add_c_ions_

bool	add_x_ions_

bool	add_z_ions_

std::string	digestion_enzyme_

EnzymaticDigestion::Specificity	enzyme_specificity_ {EnzymaticDigestion::SPEC_FULL}
	'full' (default), 'semi' (semi-tryptic), or 'none' (e.g. immunopeptidomics)

size_t	missed_cleavages_
	number of missed cleavages

float	peptide_min_mass_

float	peptide_max_mass_

size_t	peptide_min_length_

size_t	peptide_max_length_

StringList	modifications_fixed_
	Modification that are one all peptides.

StringList	modifications_variable_
	Variable Modification -> all possible comibnations are created.

size_t	max_variable_mods_per_peptide_

uint16_t	min_matched_peaks_
	PSM with less hits are discarded.

int16_t	min_isotope_error_
	Minimal possible isotope error.

int16_t	max_isotope_error_
	Maximal possible isotope error (both only used for closed search)

uint16_t	min_precursor_charge_
	minimal possible precursor charge (usually always 1)

uint16_t	max_precursor_charge_
	maximal possible precursor charge

uint16_t	max_fragment_charge_
	The maximal possible charge of the fragments.

uint32_t	max_processed_hits_
	The amount of PSM that will be used. the rest is filtered out.

Detailed Description

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.

Class Documentation

◆ OpenMS::FragmentIndex::IonOffsets

struct OpenMS::FragmentIndex::IonOffsets

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

Collaboration diagram for FragmentIndex::IonOffsets:

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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}

◆ OpenMS::FragmentIndex::SpectrumMatch

struct OpenMS::FragmentIndex::SpectrumMatch

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

Collaboration diagram for FragmentIndex::SpectrumMatch:

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Class Members
int16_t	isotope_error_ {}
uint32_t	num_matched_ {}	Number of peaks-fragment hits.
size_t	peptide_idx_ {}	< The isotope_error used for the performed search The idx this struct belongs to
uint16_t	precursor_charge_ {}	The precursor_charged used for the performed search.

◆ OpenMS::FragmentIndex::VarModEntry

struct OpenMS::FragmentIndex::VarModEntry

Entry in the per-AA variable modification lookup table.

Collaboration diagram for FragmentIndex::VarModEntry:

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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

Constructor & Destructor Documentation

◆ FragmentIndex()

FragmentIndex ( )

Default constructor.

Initializes an empty FragmentIndex. Call build() before using any query functions. After clear(), the index returns to this unbuilt state.

Thread-safety: constructing the object is thread-safe as long as the instance is not shared across threads before initialization completes.

◆ ~FragmentIndex()

~FragmentIndex ( )

overridedefault

Default destructor.

Releases owned memory. If the index was built, all internal buffers and fragment buckets are freed. No exceptions are thrown.

Member Function Documentation

◆ build()

void build ( const std::vector< FASTAFile::FASTAEntry > & fasta_entries )

Given a set of Fasta files, builds the Fragment Index datastructure (FID). First all fragments are sorted by their own mass. Next they are placed in buckets. The min-fragment mass is stored for each bucket, whereupon the fragments are sorted within the buckets by their originating precursor mass.

Parameters

[in] fasta_entries

◆ buildModSlots_()

size_t buildModSlots_	(	const char *	sequence,
		size_t	seq_len,
		ModSlot *	out_slots,
		bool	is_protein_nterm = `false`,
		bool	is_protein_cterm = `false`
	)		const

protected

Scan a peptide sequence to find all variable modification slots. Returns the number of slots written to out_slots (at most MAX_MOD_SLOTS). Deterministic ordering: N-term pure-terminal mods, then left-to-right residue mods (ANYWHERE + position-specific terminal), then C-term pure-terminal mods.

Parameters

sequence	raw amino acid character array
seq_len	length of the sequence
out_slots	output array for modification slots (must have space for MAX_MOD_SLOTS entries)
is_protein_nterm	true if this peptide starts at protein position 0
is_protein_cterm	true if this peptide ends at the last protein residue

◆ clear()

void clear ( )

Delete fragment index. Sets is_build=false.

◆ computeMassWindow_()

std::pair< float, float > computeMassWindow_ ( float precursor_mass ) const

private

Compute the signed mass window {lo, hi} around a precursor_mass, converting ppm → Da if the unit is ppm. lo is negative (or zero), hi is positive (or zero). This is the only place where positive member magnitudes become signed offsets.

◆ generateFragmentsLightweight_()

void generateFragmentsLightweight_	(	std::vector< Fragment > &	fragments,
		const char *	sequence,
		size_t	seq_len,
		UInt32	peptide_idx,
		double	n_term_mod_mass,
		double	c_term_mod_mass,
		const double *	residue_mod_masses
	)		const

protected

Lightweight fragment generation: compute b/y ion m/z directly from amino acid chars. Bypasses AASequence::fromString and TheoreticalSpectrumGenerator.

Parameters

[out]	fragments	Output vector to append Fragment entries to
[in]	sequence	Raw amino acid string (no modifications)
[in]	seq_len	Length of sequence
[in]	peptide_idx	Index of this peptide in fi_peptides_
[in]	n_term_mod_mass	Mass delta from N-terminal modification (0 if none)
[in]	c_term_mod_mass	Mass delta from C-terminal modification (0 if none)
[in]	residue_mod_masses	Per-residue modification mass deltas (nullptr if none; array of seq_len doubles)

◆ generatePeptides()

void generatePeptides ( const std::vector< FASTAFile::FASTAEntry > & fasta_entries )

protected

Generates all peptides from given fasta entries. If Bottom-up is set to false skips digestion. If set to true the Digestion enzyme can be set in the parameters. Additionally introduces fixed and variable modifications for restrictive PSM search.

Parameters

[in] fasta_entries

◆ getPeptides()

const std::vector< Peptide > & getPeptides ( ) const

Returns a reference to the internal peptide container.

Provides read-only access to all peptides currently held by the index, typically populated during build().

Returns: const reference to the internal std::vector of Peptide.

Preconditions: The vector may be empty if build() has not been called yet. Thread-safety: read-only view; safe to access concurrently as long as no thread mutates the index (e.g., build()/clear()).

◆ getPeptidesInMassWindow()

std::pair< size_t, size_t > getPeptidesInMassWindow	(	float	precursor_mass,
		const std::pair< float, float > &	window
	)		const

Return the [begin_idx, end_idx) peptide index range such that fi_peptides_[i].precursor_mz_ ∈ [precursor_mass + window.first, precursor_mass + window.second] for all i in the returned range.

Parameters

[in]	precursor_mass	The mono-charged precursor mass (M+H).
[in]	window	Signed absolute offsets around the precursor mass. By convention `window.first` is <= 0 and `window.second` is >= 0 (produced by `computeMassWindow_`). A reversed window trivially returns an empty range; no diagnostic is emitted. No hidden tolerance is added.

Returns: [begin_idx, end_idx) half-open index range into fi_peptides_.

◆ initModificationTables_()

void initModificationTables_ ( )

protected

Build per-AA modification lookup tables from modifications_fixed_ and modifications_variable_. Called once at the start of generatePeptides().

◆ initResidueMassTable_()

static void initResidueMassTable_ ( )

staticprotected

◆ isBuild()

bool isBuild ( ) const

Indicates whether the fragment index has been built.

Returns: true if build() has completed successfully and the index is ready for queries; false otherwise (e.g., after construction or after clear()).

Thread-safety: read-only and can be called concurrently with other read-only methods. Must not race with build()/clear() on the same instance.

◆ isOpenSearchMode()

static bool isOpenSearchMode	(	double	lower_magnitude,
		double	upper_magnitude,
		bool	unit_ppm
	)

inlinestaticnoexcept

Shared auto-detection: open-search iff max(lower, upper) > threshold (1000 ppm or 1 Da). Strict >: exactly 1000 ppm stays closed. This is the single source of truth for the open-search auto-detection rule and is reused by ProSEAlgorithm and the TOPP tool.

◆ isOpenSearchMode_()

bool isOpenSearchMode_ ( ) const

inlineprivatenoexcept

Instance delegate — same rule, reads the member bounds.

◆ query()

std::vector< Hit > query	(	const Peak1D &	peak,
		const std::pair< size_t, size_t > &	peptide_idx_range,
		uint16_t	peak_charge
	)

Queries one peak.

Parameters

[in]	peak	The queried peak
[in]	peptide_idx_range	The range of precursors/peptides the peptide could potentially belongs to
[in]	peak_charge	The charge of the peak. Is used to calculate the mass from the mz

Returns: a vector of Hits(matching peptide_idx_range and matching fragment_mz_) containing the idx of the hitted peptide and the mass of the hit

◆ queryPeaks()

void queryPeaks	(	SpectrumMatchesTopN &	candidates,
		const MSSpectrum &	spectrum,
		const std::pair< size_t, size_t > &	candidates_range,
		const int16_t	isotope_error,
		const uint16_t	precursor_charge
	)

private

queries peaks for a given experimental spectrum with a set range of potential peptides, isotope error and precursor charge. Hits are transferred into a PSM list. Technically an adapter between query(...) and openSearch(...)/searchDifferentPrecursorRanges(...)

Parameters

[out]	candidates	The n best Spectrum matches
[in]	spectrum	The queried experimental spectrum
[in]	candidates_range	The range of precursors/peptides the peptide could potentially belong to
[in]	isotope_error	The applied isotope error
[in]	precursor_charge	The applied precursor charge

◆ querySpectrum()

void querySpectrum	(	const MSSpectrum &	spectrum,
		SpectrumMatchesTopN &	sms
	)

: queries one complete experimental spectra against the Database. Loops over all precursor charges Starts at min_precursor_charge and iteratively goes to max_precursor_charge. We query all peaks multiple times with all the different precursor charges and corresponding precursor masses

Parameters

[in]	spectrum	experimental spectrum
[out]	sms	The n best Spectrum matches

◆ reconstructModifiedSequence()

AASequence reconstructModifiedSequence	(	const Peptide &	peptide,
		const std::vector< FASTAFile::FASTAEntry > &	fasta_entries
	)		const

Reconstruct a fully modified AASequence from a Peptide's bitmask.

Used for result output - only called for final hits (not in the build hot path). Applies fixed modifications, then uses the bitmask to determine which variable modifications are active at which positions.

Parameters

[in]	peptide	The Peptide descriptor with mod_bitmask_
[in]	fasta_entries	The FASTA database used during build()

Returns: The fully modified AASequence

◆ searchDifferentPrecursorRanges()

void searchDifferentPrecursorRanges	(	const MSSpectrum &	spectrum,
		float	precursor_mass,
		SpectrumMatchesTopN &	sms,
		uint16_t	charge
	)

private

If closed search loops over all isotope errors. For each iteration loop over all peaks with queryPeaks.

If open search applies a precursor-mass window

Parameters

[in]	spectrum	experimental query-spectrum
[in]	precursor_mass	The mass of the precursor (mz * charge)
[out]	sms	The Top m SpectrumMatches
[in]	charge	Applied charge

◆ trimHits()

void trimHits ( SpectrumMatchesTopN & init_hits ) const

private

places the k-largest elements in the front of the input array. Inside of the k-largest elements and outside the elements are not sorted

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ add_a_ions_

bool add_a_ions_

private

◆ add_b_ions_

bool add_b_ions_

private

◆ add_c_ions_

bool add_c_ions_

private

◆ add_x_ions_

bool add_x_ions_

private

◆ add_y_ions_

bool add_y_ions_

private

◆ add_z_ions_

bool add_z_ions_

private

◆ bucket_min_mz_

std::vector<float> bucket_min_mz_

protected

vector of the smalles fragment mz of each bucket

◆ bucketsize_

size_t bucketsize_

protected

number of fragments per outer node

◆ digestion_enzyme_

std::string digestion_enzyme_

private

◆ enzyme_specificity_

EnzymaticDigestion::Specificity enzyme_specificity_ {EnzymaticDigestion::SPEC_FULL}

private

'full' (default), 'semi' (semi-tryptic), or 'none' (e.g. immunopeptidomics)

◆ fi_fragments_

std::vector<Fragment> fi_fragments_

protected

vector of all theoretical fragments (b- and y- ions)

◆ fi_peptides_

std::vector<Peptide> fi_peptides_

protected

vector of all (digested) peptides

◆ fixed_cterm_delta_

double fixed_cterm_delta_ {0.0}

protected

Fixed C-terminal mod delta (0 if none)

◆ fixed_cterm_mod_ptr_

const ResidueModification* fixed_cterm_mod_ptr_ {nullptr}

protected

◆ fixed_mod_deltas_

std::array<double, 128> fixed_mod_deltas_ {}

protected

Per-AA fixed modification delta mass (0.0 if no fixed mod applies)

◆ fixed_mod_ptrs_

std::array<const ResidueModification*, 128> fixed_mod_ptrs_ {}

protected

Per-AA fixed modification pointer (nullptr if none)

◆ fixed_nterm_delta_

double fixed_nterm_delta_ {0.0}

protected

Fixed N-terminal mod delta (0 if none)

◆ fixed_nterm_mod_ptr_

const ResidueModification* fixed_nterm_mod_ptr_ {nullptr}

protected

◆ fragment_max_mz_

float fragment_max_mz_

protected

largest fragment mz

◆ fragment_min_mz_

float fragment_min_mz_

protected

smallest fragment mz

◆ fragment_mz_tolerance_

float fragment_mz_tolerance_

protected

◆ fragment_mz_tolerance_unit_ppm_

bool fragment_mz_tolerance_unit_ppm_ {true}

protected

◆ ion_offsets_

IonOffsets ion_offsets_

staticprotected

◆ is_build_

bool is_build_ {false}

protected

true, if the database has been populated with fragments

◆ mass_table_once_flag_

std::once_flag mass_table_once_flag_

staticprotected

◆ max_fragment_charge_

uint16_t max_fragment_charge_

private

The maximal possible charge of the fragments.

◆ max_isotope_error_

int16_t max_isotope_error_

private

Maximal possible isotope error (both only used for closed search)

◆ MAX_MOD_SLOTS

constexpr size_t MAX_MOD_SLOTS = 32

staticconstexprprotected

max variable mod slots per peptide (uint32_t bitmask)

◆ max_precursor_charge_

uint16_t max_precursor_charge_

private

maximal possible precursor charge

◆ max_processed_hits_

uint32_t max_processed_hits_

private

The amount of PSM that will be used. the rest is filtered out.

◆ max_variable_mods_per_peptide_

size_t max_variable_mods_per_peptide_

private

◆ min_ion_index_

size_t min_ion_index_ {0}

protected

skip ions below this index (0=all, 2=skip b1/b2/y1/y2)

◆ min_isotope_error_

int16_t min_isotope_error_

private

Minimal possible isotope error.

◆ min_matched_peaks_

uint16_t min_matched_peaks_

private

PSM with less hits are discarded.

◆ min_precursor_charge_

uint16_t min_precursor_charge_

private

minimal possible precursor charge (usually always 1)

◆ missed_cleavages_

size_t missed_cleavages_

private

number of missed cleavages

◆ mod_tables_initialized_

bool mod_tables_initialized_ {false}

protected

◆ modifications_fixed_

StringList modifications_fixed_

private

Modification that are one all peptides.

◆ modifications_variable_

StringList modifications_variable_

private

Variable Modification -> all possible comibnations are created.

◆ peptide_max_length_

size_t peptide_max_length_

private

◆ peptide_max_mass_

float peptide_max_mass_

private

◆ peptide_min_length_

size_t peptide_min_length_

private

◆ peptide_min_mass_

float peptide_min_mass_

private

◆ precursor_mass_tolerance_lower_

double precursor_mass_tolerance_lower_ {20.0}

protected

positive magnitude, effective lower bound is -lower

◆ precursor_mass_tolerance_unit_ppm_

bool precursor_mass_tolerance_unit_ppm_ {true}

protected

◆ precursor_mass_tolerance_upper_

double precursor_mass_tolerance_upper_ {20.0}

protected

positive magnitude, effective upper bound is +upper

◆ residue_mass_table_

std::array<double, 128> residue_mass_table_

staticprotected

Precomputed residue mass lookup table: ASCII char -> internal monoisotopic mass (Da). Indexed by single-letter amino acid code (e.g., 'A'=65). Entries for non-AA chars are 0.

◆ variable_cterm_mods_

std::vector<VarModEntry> variable_cterm_mods_

protected

Pure C-terminal variable mods (not residue-specific)

◆ variable_mod_table_

std::array<std::vector<VarModEntry>, 128> variable_mod_table_ {}

protected

Per-AA variable modification table: for each ASCII char, list of possible variable mods.

◆ variable_nterm_mods_

std::vector<VarModEntry> variable_nterm_mods_

protected

Pure N-terminal variable mods (not residue-specific)

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Class Documentation

◆ OpenMS::FragmentIndex::IonOffsets

◆ OpenMS::FragmentIndex::SpectrumMatch

◆ OpenMS::FragmentIndex::VarModEntry

Constructor & Destructor Documentation

◆ FragmentIndex()

◆ ~FragmentIndex()

Member Function Documentation

◆ build()

◆ buildModSlots_()

◆ clear()

◆ computeMassWindow_()

◆ generateFragmentsLightweight_()

◆ generatePeptides()

◆ getPeptides()

◆ getPeptidesInMassWindow()

◆ initModificationTables_()

◆ initResidueMassTable_()

◆ isBuild()

◆ isOpenSearchMode()

◆ isOpenSearchMode_()

◆ query()

◆ queryPeaks()

◆ querySpectrum()

◆ reconstructModifiedSequence()

◆ searchDifferentPrecursorRanges()

◆ trimHits()

◆ updateMembers_()

Member Data Documentation

◆ add_a_ions_

◆ add_b_ions_

◆ add_c_ions_

◆ add_x_ions_

◆ add_y_ions_

◆ add_z_ions_

◆ bucket_min_mz_

◆ bucketsize_

◆ digestion_enzyme_

◆ enzyme_specificity_

◆ fi_fragments_

◆ fi_peptides_

◆ fixed_cterm_delta_

◆ fixed_cterm_mod_ptr_

◆ fixed_mod_deltas_

◆ fixed_mod_ptrs_

◆ fixed_nterm_delta_

◆ fixed_nterm_mod_ptr_

◆ fragment_max_mz_

◆ fragment_min_mz_

◆ fragment_mz_tolerance_

◆ fragment_mz_tolerance_unit_ppm_

◆ ion_offsets_

◆ is_build_

◆ mass_table_once_flag_

◆ max_fragment_charge_

◆ max_isotope_error_

◆ MAX_MOD_SLOTS

◆ max_precursor_charge_

◆ max_processed_hits_

◆ max_variable_mods_per_peptide_

◆ min_ion_index_

◆ min_isotope_error_

◆ min_matched_peaks_

◆ min_precursor_charge_

◆ missed_cleavages_

◆ mod_tables_initialized_

◆ modifications_fixed_

◆ modifications_variable_

◆ peptide_max_length_

◆ peptide_max_mass_