FragmentIndex Class Reference

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:

Collaboration diagram for FragmentIndex:

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

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 >	getPeptidesInPrecursorRange (float precursor_mass, const std::pair< float, float > &window)
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
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.

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

Protected Attributes
bool	is_build_ {false}
	true, if the database has been populated with fragments
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	bucketsize_
	number of fragments per outer node
std::vector< float >	bucket_min_mz_
	vector of the smalles fragment mz of each bucket
float	precursor_mz_tolerance_
bool	precursor_mz_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;.

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
	Helper function to determine if open search should be used based on tolerance.

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_
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.
float	open_precursor_window_lower_
	Defines the lower bound of the precursor-mass range.
float	open_precursor_window_upper_
	Defines the upper bound of the precursor-mass range.

Additional Inherited Members
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.

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.

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Class Documentation

OpenMS::FragmentIndex::SpectrumMatch

struct OpenMS::FragmentIndex::SpectrumMatch

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

Collaboration diagram for FragmentIndex::SpectrumMatch:

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.

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

clear()

void clear

(

)

Delete fragment index. Sets is_build=false.

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()).

getPeptidesInPrecursorRange()

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

Return index range of all possible Peptides/Proteins, such that a vector can be created fitting that range (safe some memory)

Parameters

[in]	precursor_mass	The mono-charged precursor mass (M+H)
[in]	window	Defines the lower and upper bound for the precusor mass. For closed search it only contains the tolerance. In case of open search it contains both tolerance and open-search-window

Returns

a pair of indexes defining all possible peptides which the current peak could hit

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_()

bool isOpenSearchMode_ ( ) const

inlineprivate

Helper function to determine if open search should be used based on tolerance.

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

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

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

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

is_build_

bool is_build_ {false}

protected

true, if the database has been populated with fragments

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_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_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

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.

open_precursor_window_lower_

float open_precursor_window_lower_

private

Defines the lower bound of the precursor-mass range.

open_precursor_window_upper_

float open_precursor_window_upper_

private

Defines the upper bound of the precursor-mass range.

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_mz_tolerance_

float precursor_mz_tolerance_

protected

precursor_mz_tolerance_unit_ppm_

bool precursor_mz_tolerance_unit_ppm_ {true}

protected