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

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

Inheritance 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 ()
virtual	~PSLPFormulation ()
template<typename InputPeakType >
void	createAndSolveILPForKnownLCMSMapFeatureBased (const FeatureMap<> &features, const MSExperiment< InputPeakType > &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.
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.
template<typename InputPeakType >
void	createAndSolveCombinedLPForKnownLCMSMapFeatureBased (const FeatureMap<> &features, const MSExperiment< InputPeakType > &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.
void	setLPSolver (LPWrapper::SOLVER solver)
LPWrapper::SOLVER	getLPSolver ()
template<typename InputPeakType >
void	createAndSolveCombinedLPForKnownLCMSMapFeatureBased (const FeatureMap<> &features, const MSExperiment< InputPeakType > &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, bool sequential_order)
Protected Member Functions
template<typename InputPeakType >
void	getXIC_ (const std::vector< std::pair< Size, Size > > &end_points, std::vector< DoubleReal > &weights, const MSExperiment< InputPeakType > &experiment, const bool normalize)
template<typename InputPeakType >
void	calculateXICs_ (std::vector< std::vector< DoubleReal > > &xics, const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const bool normalize)
	Calculates the XICs for all features.
void	createAndSolveILP_ (const FeatureMap<> &features, std::vector< std::vector< DoubleReal > > &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.
void	createAndSolveCombinedLPFeatureBased_ (const FeatureMap<> &features, std::vector< std::vector< DoubleReal > > &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< DoubleReal > >::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_ (String acc, FeatureMap<> &features, PrecursorIonSelectionPreprocessing &preprocessed_db, std::vector< IndexTriple > &variable_indices)
Int	getNumberOfPrecsInSpectrum_ (Int constr_idx)
Protected Attributes
LPWrapper *	model_
LPWrapper::SOLVER	solver_

Detailed Description

Implements ILP formulation of precursor selection problems.

Constructor & Destructor Documentation

PSLPFormulation ( )

virtual ~PSLPFormulation ( ) [virtual]

Member Function Documentation

void addMaxInclusionListSizeConstraints_	(	std::vector< IndexTriple > &	variable_indices,
		UInt	max_list_size
	)			`[protected]`

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

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

void addProteinToILP_	(	PrecursorIonSelectionPreprocessing &	preprocessing,
		std::map< String, std::vector< DoubleReal > >::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]`

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

void addStepSizeConstraint_	(	std::vector< IndexTriple > &	variable_indices,
		UInt	step_size
	)			`[protected]`

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

void calculateXICs_	(	std::vector< std::vector< DoubleReal > > &	xics,
		const FeatureMap<> &	features,
		const MSExperiment< InputPeakType > &	experiment,
		const std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		const bool	normalize
	)			`[protected]`

Calculates the XICs for all features.

References PSLPFormulation::getXIC_().

Referenced by PSLPFormulation::createAndSolveCombinedLPForKnownLCMSMapFeatureBased(), and PSLPFormulation::createAndSolveILPForKnownLCMSMapFeatureBased().

void createAndSolveCombinedLPFeatureBased_	(	const FeatureMap<> &	features,
		std::vector< std::vector< DoubleReal > > &	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]`

Referenced by PSLPFormulation::createAndSolveCombinedLPForKnownLCMSMapFeatureBased().

void createAndSolveCombinedLPForKnownLCMSMapFeatureBased	(	const FeatureMap<> &	features,
		const MSExperiment< InputPeakType > &	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,
		bool	sequential_order
	)

References PSLPFormulation::calculateXICs_(), and PSLPFormulation::createAndSolveCombinedLPFeatureBased_().

void createAndSolveCombinedLPForKnownLCMSMapFeatureBased	(	const FeatureMap<> &	features,
		const MSExperiment< InputPeakType > &	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 createAndSolveILP_	(	const FeatureMap<> &	features,
		std::vector< std::vector< DoubleReal > > &	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.

Referenced by PSLPFormulation::createAndSolveILPForKnownLCMSMapFeatureBased().

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.

void createAndSolveILPForKnownLCMSMapFeatureBased	(	const FeatureMap<> &	features,
		const MSExperiment< InputPeakType > &	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

References PSLPFormulation::calculateXICs_(), and PSLPFormulation::createAndSolveILP_().

Referenced by OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap().

LPWrapper::SOLVER getLPSolver ( ) [inline]

Int getNumberOfPrecsInSpectrum_ ( Int constr_idx ) [protected]

void getXIC_	(	const std::vector< std::pair< Size, Size > > &	end_points,
		std::vector< DoubleReal > &	weights,
		const MSExperiment< InputPeakType > &	experiment,
		const bool	normalize
	)			`[protected]`

Referenced by PSLPFormulation::calculateXICs_().

void setLPSolver ( LPWrapper::SOLVER solver ) [inline]

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

Solve the ILP.

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

void updateObjFunction_	(	String	acc,
		FeatureMap<> &	features,
		PrecursorIonSelectionPreprocessing &	preprocessed_db,
		std::vector< IndexTriple > &	variable_indices
	)			`[protected]`

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

void updateStepSizeConstraint	(	Size	iteration,
		UInt	step_size
	)

Member Data Documentation

LPWrapper* model_ [protected]

LPWrapper::SOLVER solver_ [protected]

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1

PSLPFormulation Class Reference

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation