Implements ILP formulation of precursor selection problems. More...

#include <OpenMS/ANALYSIS/TARGETED/PSLPFormulation.h>

Inheritance diagram for PSLPFormulation:

Collaboration diagram for PSLPFormulation:

Classes
struct	IndexLess

struct	IndexTriple
	Struct that holds the indices of the precursors in the feature map and the ilp formulation. More...

struct	ScanLess

struct	VariableIndexLess

Public Member Functions
	PSLPFormulation ()

	~PSLPFormulation () override

void	createAndSolveILPForKnownLCMSMapFeatureBased (const FeatureMap &features, const PeakMap &experiment, std::vector< IndexTriple > &variable_indices, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::set< Int > &charges_set, UInt ms2_spectra_per_rt_bin, std::vector< int > &solution_indices)
	Encode ILP formulation for a given LC-MS map, but unknown protein sample. More...

void	createAndSolveILPForInclusionListCreation (PrecursorIonSelectionPreprocessing &preprocessing, UInt ms2_spectra_per_rt_bin, UInt max_list_size, FeatureMap &precursors, bool solve_ILP=true)
	Find a set of precursors, so that the protein coverage is maximal and that the number of precursors per bin is not exceeded. More...

void	createAndSolveCombinedLPForKnownLCMSMapFeatureBased (const FeatureMap &features, const PeakMap &experiment, std::vector< IndexTriple > &variable_indices, std::vector< int > &solution_indices, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::set< Int > &charges_set, UInt ms2_spectra_per_rt_bin, Size step_size=0, bool sequential_order=false)

void	updateStepSizeConstraint (Size iteration, UInt step_size)

void	updateFeatureILPVariables (FeatureMap &new_features, std::vector< IndexTriple > &variable_indices, std::map< Size, std::vector< String > > &feature_constraints_map)

void	updateRTConstraintsForSequentialILP (Size &rt_index, UInt ms2_spectra_per_rt_bin, Size max_rt_index)

void	updateCombinedILP (FeatureMap &features, PrecursorIonSelectionPreprocessing &preprocessed_db, std::vector< IndexTriple > &variable_indices, std::vector< String > &new_protein_accs, std::vector< String > &protein_accs, PSProteinInference &prot_inference, Size &variable_counter, std::map< String, std::vector< Size > > &protein_feature_map, Feature &new_feature, std::map< String, Size > &protein_variable_index_map, std::map< String, std::set< String > > &prot_id_counter)

void	solveILP (std::vector< int > &solution_indices)
	Solve the ILP. More...

void	setLPSolver (LPWrapper::SOLVER solver)

LPWrapper::SOLVER	getLPSolver ()

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

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

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

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

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

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

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

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

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

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

Protected Member Functions
void	getXIC_ (const std::vector< std::pair< Size, Size > > &end_points, std::vector< double > &weights, const PeakMap &experiment, const bool normalize)

void	calculateXICs_ (std::vector< std::vector< double > > &xics, const FeatureMap &features, const PeakMap &experiment, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const bool normalize)
	Calculates the XICs for all features. More...

void	createAndSolveILP_ (const FeatureMap &features, std::vector< std::vector< double > > &intensity_weights, std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::vector< IndexTriple > &variable_indices, std::vector< int > &solution_indices, UInt ms2_spectra_per_rt_bin, Size number_of_scans)
	Creates and solves the ILP. More...

void	createAndSolveCombinedLPFeatureBased_ (const FeatureMap &features, std::vector< std::vector< double > > &intensity_weights, std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::vector< IndexTriple > &variable_indices, std::vector< Int > &solution_indices, UInt ms2_spectra_per_rt_bin, Size number_of_scans, Size step_size=0, bool sequential_order=false)

void	addProteinToILP_ (PrecursorIonSelectionPreprocessing &preprocessing, std::map< String, std::vector< double > >::const_iterator map_iter, Size &counter, Size &pep_counter, Size &feature_counter, std::vector< IndexTriple > &variable_indices, std::map< String, Size > &protein_penalty_index_map, FeatureMap &precursors)

void	addPrecursorAcquisitionNumberConstraint_ (std::vector< IndexTriple > &variable_indices, Size number_of_features, UInt number_of_msms_per_precursor)

void	addMaxInclusionListSizeConstraints_ (std::vector< IndexTriple > &variable_indices, UInt max_list_size)

void	addRTBinCapacityConstraint_ (std::vector< IndexTriple > &variable_indices, Size max_rt_index, UInt ms2_spectra_per_rt_bin, bool sequential_order=false)

void	addProteinCoverageConstraint_ (std::vector< IndexTriple > &variable_indices, PrecursorIonSelectionPreprocessing &preprocessing, std::map< String, Size > protein_variable_index_map)

void	addStepSizeConstraint_ (std::vector< IndexTriple > &variable_indices, UInt step_size)

void	assembleInclusionListForProteinBasedLP_ (std::vector< IndexTriple > &variable_indices, FeatureMap &precursors, std::vector< int > &solution_indices, PrecursorIonSelectionPreprocessing &preprocessing)

void	updateObjFunction_ (const String &acc, FeatureMap &features, PrecursorIonSelectionPreprocessing &preprocessed_db, std::vector< IndexTriple > &variable_indices)

Int	getNumberOfPrecsInSpectrum_ (Int constr_idx)

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
LPWrapper *	model_

LPWrapper::SOLVER	solver_

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

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

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

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

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

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

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. More...

Detailed Description

Implements ILP formulation of precursor selection problems.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
mz_tolerance	float	25.0	min: 0.0	Allowed precursor mass error tolerance in ppm.
rt:min_rt	float	960.0	min: 0.0	Minimal rt in seconds.
rt:max_rt	float	3840.0	min: 0.0	Maximal rt in seconds.
rt:rt_step_size	float	30.0	min: 1.0	rt step size in seconds.
rt:rt_window_size	int	100	min: 1	rt window size in seconds.
thresholds:min_protein_probability	float	0.2	min: 0.0 max: 1.0	Minimal protein probability for a protein to be considered in the ILP
thresholds:min_protein_id_probability	float	0.95	min: 0.0 max: 1.0	Minimal protein probability for a protein to be considered identified.
thresholds:min_pt_weight	float	0.5	min: 0.0 max: 1.0	Minimal pt weight of a precursor
thresholds:min_mz	float	500.0	min: 0.0	Minimal mz to be considered in protein based LP formulation.
thresholds:max_mz	float	5000.0	min: 0.0	Minimal mz to be considered in protein based LP formulation.
thresholds:min_pred_pep_prob	float	0.5	min: 0.0 max: 1.0	Minimal predicted peptide probability of a precursor
thresholds:min_rt_weight	float	0.5	min: 0.0 max: 1.0	Minimal rt weight of a precursor
thresholds:use_peptide_rule	string	false	true, false	Use peptide rule instead of minimal protein id probability
thresholds:min_peptide_ids	int	2	min: 1	If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id
thresholds:min_peptide_probability	float	0.95	min: 0.0 max: 1.0	If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified
combined_ilp:k1	float	0.2	min: 0.0	combined ilp: weight for z_i
combined_ilp:k2	float	0.2	min: 0.0	combined ilp: weight for x_j,s*int_j,s
combined_ilp:k3	float	0.4	min: 0.0	combined ilp: weight for -x_j,s*w_j,s
combined_ilp:scale_matching_probs	string	true	true, false	flag if detectability * rt_weight shall be scaled to cover all [0,1]
feature_based:no_intensity_normalization	string	false	true, false	Flag indicating if intensities shall be scaled to be in [0,1]. This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1.
feature_based:max_number_precursors_per_feature	int	1	min: 1	The maximal number of precursors per feature.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Class Documentation

◆ OpenMS::PSLPFormulation::IndexTriple

struct OpenMS::PSLPFormulation::IndexTriple

Struct that holds the indices of the precursors in the feature map and the ilp formulation.

Collaboration diagram for PSLPFormulation::IndexTriple:

[legend]

Class Members
Size	feature
String	prot_acc
double	rt_probability
Int	scan
double	signal_weight
Size	variable

Constructor & Destructor Documentation

◆ PSLPFormulation()

PSLPFormulation ( )

◆ ~PSLPFormulation()

~PSLPFormulation ( )

override

Member Function Documentation

◆ addMaxInclusionListSizeConstraints_()

void addMaxInclusionListSizeConstraints_	(	std::vector< IndexTriple > &	variable_indices,
		UInt	max_list_size
	)

protected

◆ addPrecursorAcquisitionNumberConstraint_()

void addPrecursorAcquisitionNumberConstraint_	(	std::vector< IndexTriple > &	variable_indices,
		Size	number_of_features,
		UInt	number_of_msms_per_precursor
	)

protected

◆ addProteinCoverageConstraint_()

void addProteinCoverageConstraint_	(	std::vector< IndexTriple > &	variable_indices,
		PrecursorIonSelectionPreprocessing &	preprocessing,
		std::map< String, Size >	protein_variable_index_map
	)

protected

◆ addProteinToILP_()

void addProteinToILP_	(	PrecursorIonSelectionPreprocessing &	preprocessing,
		std::map< String, std::vector< double > >::const_iterator	map_iter,
		Size &	counter,
		Size &	pep_counter,
		Size &	feature_counter,
		std::vector< IndexTriple > &	variable_indices,
		std::map< String, Size > &	protein_penalty_index_map,
		FeatureMap &	precursors
	)

protected

◆ addRTBinCapacityConstraint_()

void addRTBinCapacityConstraint_	(	std::vector< IndexTriple > &	variable_indices,
		Size	max_rt_index,
		UInt	ms2_spectra_per_rt_bin,
		bool	sequential_order = `false`
	)

protected

◆ addStepSizeConstraint_()

void addStepSizeConstraint_	(	std::vector< IndexTriple > &	variable_indices,
		UInt	step_size
	)

protected

◆ assembleInclusionListForProteinBasedLP_()

void assembleInclusionListForProteinBasedLP_	(	std::vector< IndexTriple > &	variable_indices,
		FeatureMap &	precursors,
		std::vector< int > &	solution_indices,
		PrecursorIonSelectionPreprocessing &	preprocessing
	)

protected

◆ calculateXICs_()

void calculateXICs_	(	std::vector< std::vector< double > > &	xics,
		const FeatureMap &	features,
		const PeakMap &	experiment,
		const std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		const bool	normalize
	)

protected

Calculates the XICs for all features.

◆ createAndSolveCombinedLPFeatureBased_()

void createAndSolveCombinedLPFeatureBased_	(	const FeatureMap &	features,
		std::vector< std::vector< double > > &	intensity_weights,
		std::set< Int > &	charges_set,
		std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		std::vector< IndexTriple > &	variable_indices,
		std::vector< Int > &	solution_indices,
		UInt	ms2_spectra_per_rt_bin,
		Size	number_of_scans,
		Size	step_size = `0`,
		bool	sequential_order = `false`
	)

protected

◆ createAndSolveCombinedLPForKnownLCMSMapFeatureBased()

void createAndSolveCombinedLPForKnownLCMSMapFeatureBased	(	const FeatureMap &	features,
		const PeakMap &	experiment,
		std::vector< IndexTriple > &	variable_indices,
		std::vector< int > &	solution_indices,
		std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		std::set< Int > &	charges_set,
		UInt	ms2_spectra_per_rt_bin,
		Size	step_size = `0`,
		bool	sequential_order = `false`
	)

◆ createAndSolveILP_()

void createAndSolveILP_	(	const FeatureMap &	features,
		std::vector< std::vector< double > > &	intensity_weights,
		std::set< Int > &	charges_set,
		std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		std::vector< IndexTriple > &	variable_indices,
		std::vector< int > &	solution_indices,
		UInt	ms2_spectra_per_rt_bin,
		Size	number_of_scans
	)

protected

Creates and solves the ILP.

◆ createAndSolveILPForInclusionListCreation()

void createAndSolveILPForInclusionListCreation	(	PrecursorIonSelectionPreprocessing &	preprocessing,
		UInt	ms2_spectra_per_rt_bin,
		UInt	max_list_size,
		FeatureMap &	precursors,
		bool	solve_ILP = `true`
	)

Find a set of precursors, so that the protein coverage is maximal and that the number of precursors per bin is not exceeded.

◆ createAndSolveILPForKnownLCMSMapFeatureBased()

void createAndSolveILPForKnownLCMSMapFeatureBased	(	const FeatureMap &	features,
		const PeakMap &	experiment,
		std::vector< IndexTriple > &	variable_indices,
		std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		std::set< Int > &	charges_set,
		UInt	ms2_spectra_per_rt_bin,
		std::vector< int > &	solution_indices
	)

Encode ILP formulation for a given LC-MS map, but unknown protein sample.

Parameters

features	FeatureMap with all possible precursors
experiment	Input raw data
variable_indices	Assignment of feature indices and ILP variables
mass_ranges	Feature borders as indices in the raw data
charges_set	Allowed charge states
ms2_spectra_per_rt_bin	Allowed number of precursors per rt bin
solution_indices	Indices of ILP variables that are in the optimal solution

◆ getLPSolver()

LPWrapper::SOLVER getLPSolver ( )

inline

◆ getNumberOfPrecsInSpectrum_()

Int getNumberOfPrecsInSpectrum_ ( Int constr_idx )

protected

◆ getXIC_()

void getXIC_	(	const std::vector< std::pair< Size, Size > > &	end_points,
		std::vector< double > &	weights,
		const PeakMap &	experiment,
		const bool	normalize
	)

protected

◆ setLPSolver()

void setLPSolver ( LPWrapper::SOLVER solver )

inline

◆ solveILP()

void solveILP ( std::vector< int > & solution_indices )

Solve the ILP.

◆ updateCombinedILP()

void updateCombinedILP	(	FeatureMap &	features,
		PrecursorIonSelectionPreprocessing &	preprocessed_db,
		std::vector< IndexTriple > &	variable_indices,
		std::vector< String > &	new_protein_accs,
		std::vector< String > &	protein_accs,
		PSProteinInference &	prot_inference,
		Size &	variable_counter,
		std::map< String, std::vector< Size > > &	protein_feature_map,
		Feature &	new_feature,
		std::map< String, Size > &	protein_variable_index_map,
		std::map< String, std::set< String > > &	prot_id_counter
	)

◆ updateFeatureILPVariables()

void updateFeatureILPVariables	(	FeatureMap &	new_features,
		std::vector< IndexTriple > &	variable_indices,
		std::map< Size, std::vector< String > > &	feature_constraints_map
	)

◆ updateObjFunction_()

void updateObjFunction_	(	const String &	acc,
		FeatureMap &	features,
		PrecursorIonSelectionPreprocessing &	preprocessed_db,
		std::vector< IndexTriple > &	variable_indices
	)

protected

◆ updateRTConstraintsForSequentialILP()

void updateRTConstraintsForSequentialILP	(	Size &	rt_index,
		UInt	ms2_spectra_per_rt_bin,
		Size	max_rt_index
	)

◆ updateStepSizeConstraint()

void updateStepSizeConstraint	(	Size	iteration,
		UInt	step_size
	)

Member Data Documentation

◆ model_

LPWrapper* model_

protected

◆ solver_

LPWrapper::SOLVER solver_

protected

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::PSLPFormulation::IndexTriple

Constructor & Destructor Documentation

◆ PSLPFormulation()

◆ ~PSLPFormulation()

Member Function Documentation

◆ addMaxInclusionListSizeConstraints_()

◆ addPrecursorAcquisitionNumberConstraint_()

◆ addProteinCoverageConstraint_()

◆ addProteinToILP_()

◆ addRTBinCapacityConstraint_()

◆ addStepSizeConstraint_()

◆ assembleInclusionListForProteinBasedLP_()

◆ calculateXICs_()

◆ createAndSolveCombinedLPFeatureBased_()

◆ createAndSolveCombinedLPForKnownLCMSMapFeatureBased()

◆ createAndSolveILP_()

◆ createAndSolveILPForInclusionListCreation()

◆ createAndSolveILPForKnownLCMSMapFeatureBased()

◆ getLPSolver()

◆ getNumberOfPrecsInSpectrum_()

◆ getXIC_()

◆ setLPSolver()

◆ solveILP()

◆ updateCombinedILP()

◆ updateFeatureILPVariables()

◆ updateObjFunction_()

◆ updateRTConstraintsForSequentialILP()

◆ updateStepSizeConstraint()

Member Data Documentation

◆ model_

◆ solver_