- backwardReachableSet(BDD) - Method in class mx.unam.iimas.griffin.grn.util.SteadyStateAnalyzer
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Obtains the backward reachable set for the provided BDD
- Basins - Class in mx.unam.iimas.griffin.grn.explorer
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Basins of attraction
- Basins() - Constructor for class mx.unam.iimas.griffin.grn.explorer.Basins
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- BDDBooleanNetworkModule - Class in mx.unam.iimas.griffin.grn.util
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A BDD interface related to a Boolean Network
- BDDBooleanNetworkModule(BooleanGeneRegulatoryNetwork) - Constructor for class mx.unam.iimas.griffin.grn.util.BDDBooleanNetworkModule
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Creates the Binary Decision Diagram interface for the provided Boolean
network
- BDDModule - Class in mx.unam.iimas.griffin.bdd
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Binary Decision Diagram Wrapper for BeeDeeDee
The module allows for encoding and decoding from Boolean Formulas represented
as sentence trees
- BDDModule() - Constructor for class mx.unam.iimas.griffin.bdd.BDDModule
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Creates the module
- BinaryFormula - Class in mx.unam.iimas.griffin.logic
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- BinaryFormula(Formula, Formula) - Constructor for class mx.unam.iimas.griffin.logic.BinaryFormula
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Creates a the formula with a binary operator
- BinaryOperation - Interface in mx.unam.iimas.griffin.logic
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Binary operation
- block(PropositionalModel, ISolver, Map<Variable, Integer>) - Method in class mx.unam.iimas.griffin.grn.explorer.topology.StructureBlocker
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- block(List<Literal>, ISolver, Map<Variable, Integer>) - Method in class mx.unam.iimas.griffin.grn.explorer.topology.StructureBlocker
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- block(PropositionalModel, ISolver, Map<Variable, Integer>) - Method in interface mx.unam.iimas.griffin.sat.ClauseBlocker
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Prunes the satisfying assignments by adding blocking clauses according to
the given model
- block(List<Literal>, ISolver, Map<Variable, Integer>) - Method in interface mx.unam.iimas.griffin.sat.ClauseBlocker
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Prunes the satisfying assignments by adding blocking clauses according to
the given list of literals assignment
- block(PropositionalModel, ISolver, Map<Variable, Integer>) - Method in class mx.unam.iimas.griffin.sat.DefaultModelBlocker
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- block(List<Literal>, ISolver, Map<Variable, Integer>) - Method in class mx.unam.iimas.griffin.sat.DefaultModelBlocker
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- blockAssignment(List<Literal>) - Method in interface mx.unam.iimas.griffin.sat.AllSATSolver
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Blocks the given assignment
- blockAssignment(List<Literal>) - Method in class mx.unam.iimas.griffin.sat.ModelIterator
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- blockAttractor(ModelIterator, BooleanNetworkStateTrajectory, Map<Gene, Set<Gene>>) - Static method in class mx.unam.iimas.griffin.grn.explorer.attractor.AttractorUtil
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A posteriori attractor blocking
- blockAttractors(ModelIterator, Set<BooleanNetworkStateTrajectory>, Map<Gene, Set<Gene>>) - Static method in class mx.unam.iimas.griffin.grn.explorer.attractor.AttractorUtil
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Blocks the particular set of attractors provided
- BOOLEAN_STATE - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
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Regular expression matching a boolean state
- BooleanConstant - Class in mx.unam.iimas.griffin.logic
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A boolean value true or false
- BooleanConstant(boolean) - Constructor for class mx.unam.iimas.griffin.logic.BooleanConstant
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Creates the boolean value
- BooleanExpressionParser - Interface in mx.unam.iimas.griffin.logic.parser
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Parser for boolean expressions
- BooleanGeneRegulatoryNetwork - Class in mx.unam.iimas.griffin.grn
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Boolean regulatory network
- BooleanGeneRegulatoryNetwork(Set<StateTransitionRule>) - Constructor for class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetwork
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Creates the gene regulatory network
- BooleanGeneRegulatoryNetworkInfo - Class in mx.unam.iimas.griffin.grn
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Information about a Boolean Gene Regulatory Network
- BooleanGeneRegulatoryNetworkInfo() - Constructor for class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetworkInfo
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Creates the network info
- BooleanGeneRegulatoryNetworkInfo(String, String) - Constructor for class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetworkInfo
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Creates the object with the specified parameters
- BooleanNetworkState - Class in mx.unam.iimas.griffin.grn
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Boolean state of a set of genes
A set of genes, each of which is either expressed or not expressed
- BooleanNetworkState(int) - Constructor for class mx.unam.iimas.griffin.grn.BooleanNetworkState
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Creates a new boolean network state
- BooleanNetworkStateSetValue - Class in mx.unam.iimas.griffin.grn.explorer.io
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Set of Boolean network state
- BooleanNetworkStateSetValue(String, Map<Integer, Gene>) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.BooleanNetworkStateSetValue
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Creates the value for the given input
- BooleanNetworkStateTrajectory - Class in mx.unam.iimas.griffin.grn
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Boolean network state trajectory
An ordered list of states
- BooleanNetworkStateTrajectory(List<BooleanNetworkState>, Boolean) - Constructor for class mx.unam.iimas.griffin.grn.BooleanNetworkStateTrajectory
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Creates the trajectory
- BooleanNetworkStateTrajectory(BooleanNetworkState) - Constructor for class mx.unam.iimas.griffin.grn.BooleanNetworkStateTrajectory
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Creates a loop trajectory
- BooleanNetworkTruthTableFileParser - Class in mx.unam.iimas.griffin.grn.explorer.io
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Parses a file representing a Boolean Network as a truth table
- BooleanNetworkTruthTableFileParser() - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.BooleanNetworkTruthTableFileParser
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- byAcronym(String) - Static method in enum mx.unam.iimas.griffin.grn.GeneInteractionType
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Obtains the type of the acronym provided