PSLPFormulation

class pyopenms.PSLPFormulation

Bases: object

Cython implementation of _PSLPFormulation

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1PSLPFormulation.html

– Inherits from [‘DefaultParamHandler’]

__init__()

  • Cython signature: void PSLPFormulation()

  • Cython signature: void PSLPFormulation(PSLPFormulation &)

Methods

__init__

  • Cython signature: void PSLPFormulation()

createAndSolveILPForInclusionListCreation

Cython signature: void createAndSolveILPForInclusionListCreation(PrecursorIonSelectionPreprocessing & preprocessing, unsigned int ms2_spectra_per_rt_bin, unsigned int max_list_size, FeatureMap & precursors, bool solve_ILP) Find a set of precursors, so that the protein coverage is maximal and that the number of precursors per bin is not exceeded

createAndSolveILPForKnownLCMSMapFeatureBased

Cython signature: void createAndSolveILPForKnownLCMSMapFeatureBased(FeatureMap & features, MSExperiment & experiment, libcpp_vector[IndexTriple] & variable_indices, libcpp_vector[libcpp_vector[libcpp_pair[size_t,size_t]]] & mass_ranges, libcpp_set[int] & charges_set, unsigned int ms2_spectra_per_rt_bin, libcpp_vector[int] & solution_indices)

getDefaults

Cython signature: Param getDefaults() Returns the default parameters

getLPSolver

Cython signature: SOLVER getLPSolver()

getName

Cython signature: String getName() Returns the name

getParameters

Cython signature: Param getParameters() Returns the parameters

getSubsections

Cython signature: libcpp_vector[String] getSubsections()

setLPSolver

Cython signature: void setLPSolver(SOLVER solver)

setName

Cython signature: void setName(const String &) Sets the name

setParameters

Cython signature: void setParameters(Param & param) Sets the parameters

solveILP

Cython signature: void solveILP(libcpp_vector[int] & solution_indices) Solve the ILP

updateRTConstraintsForSequentialILP

Cython signature: void updateRTConstraintsForSequentialILP(size_t & rt_index, unsigned int ms2_spectra_per_rt_bin, size_t max_rt_index)

updateStepSizeConstraint

Cython signature: void updateStepSizeConstraint(size_t iteration, unsigned int step_size)
createAndSolveILPForInclusionListCreation()

Cython signature: void createAndSolveILPForInclusionListCreation(PrecursorIonSelectionPreprocessing & preprocessing, unsigned int ms2_spectra_per_rt_bin, unsigned int max_list_size, FeatureMap & precursors, bool solve_ILP) Find a set of precursors, so that the protein coverage is maximal and that the number of precursors per bin is not exceeded

createAndSolveILPForKnownLCMSMapFeatureBased()

Cython signature: void createAndSolveILPForKnownLCMSMapFeatureBased(FeatureMap & features, MSExperiment & experiment, libcpp_vector[IndexTriple] & variable_indices, libcpp_vector[libcpp_vector[libcpp_pair[size_t,size_t]]] & mass_ranges, libcpp_set[int] & charges_set, unsigned int ms2_spectra_per_rt_bin, libcpp_vector[int] & solution_indices)

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

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getLPSolver()

Cython signature: SOLVER getLPSolver()

getName()

Cython signature: String getName() Returns the name

getParameters()

Cython signature: Param getParameters() Returns the parameters

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

setLPSolver()

Cython signature: void setLPSolver(SOLVER solver)

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters

solveILP()

Cython signature: void solveILP(libcpp_vector[int] & solution_indices) Solve the ILP

updateRTConstraintsForSequentialILP()

Cython signature: void updateRTConstraintsForSequentialILP(size_t & rt_index, unsigned int ms2_spectra_per_rt_bin, size_t max_rt_index)

updateStepSizeConstraint()

Cython signature: void updateStepSizeConstraint(size_t iteration, unsigned int step_size)