- Ejemplo3Genes - Class in mx.unam.iimas.griffin.grn.models
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- Ejemplo3Genes() - Constructor for class mx.unam.iimas.griffin.grn.models.Ejemplo3Genes
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Construye la red
- encode(Map<Variable, Variable>) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
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Encodes the rewriting map using the corresponding identifiers
- encode() - Method in class mx.unam.iimas.griffin.grn.code.analysis.KlarnerEncoder
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Obtains a Boolean expression representing all Klarner's constraints
- encode(Set<Gene>, Set<BooleanNetworkState>, Map<Gene, Set<Gene>>, boolean) - Static method in class mx.unam.iimas.griffin.grn.code.FixedPointAttractorEncoder
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Encodes the set of states giving the provided dependencies
- encode(BooleanNetworkState, Set<Gene>, Map<Gene, Set<Gene>>) - Static method in class mx.unam.iimas.griffin.grn.code.FixedPointAttractorEncoder
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Encodes the given state
- encode(GeneRegulation, Set<Gene>) - Static method in class mx.unam.iimas.griffin.grn.code.GeneInteractionEncoder
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Encodes the given regulation
- encode(Set<GeneInteraction>, Map<Gene, Set<Gene>>) - Static method in class mx.unam.iimas.griffin.grn.code.GeneInteractionEncoder
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Encodes the set of gene interactions as a boolean expression
- encode(Set<GeneInteraction>) - Static method in class mx.unam.iimas.griffin.grn.code.GeneInteractionEncoder
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Encodes the set of gene interactions.
- encode(GeneInteraction, Set<Gene>) - Static method in class mx.unam.iimas.griffin.grn.code.GeneInteractionEncoder
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Encodes the given gene interaction
- encode(Set<Gene>, Set<GeneInteraction>, Set<BooleanNetworkState>, GeneRegulationDeterministicEncoder.StableStatesPolicy) - Static method in class mx.unam.iimas.griffin.grn.code.GeneInteractionQueryEncoder
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Encodes the given set of gene interactions
- encode() - Method in class mx.unam.iimas.griffin.grn.code.GeneRegulationDeterministicEncoder
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- encode() - Method in interface mx.unam.iimas.griffin.grn.code.GeneRegulationEncoder
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Encodes the gene regulation specification as a boolean tree sentence
- encode() - Method in class mx.unam.iimas.griffin.grn.code.GeneRegulationQueryEncoder
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Encodes a boolean expression for identifying regulations in a given
network
- encode(Set<InputOutputStatePair>, GeneRegulationSpecification, GeneRegulationDeterministicEncoder.HypotheticalRegulationPolicy) - Static method in class mx.unam.iimas.griffin.grn.code.InputOutputEncoder
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Encodes the input-output state pairs
- encode(Set<InputOutputStatePair>, Map<Gene, Set<Gene>>) - Static method in class mx.unam.iimas.griffin.grn.code.InputOutputEncoder
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Encodes the input-output state pairs
- encode(Set<MutantExperiment>, Map<Gene, Set<Gene>>, Set<BooleanNetworkState>) - Static method in class mx.unam.iimas.griffin.grn.code.MutantExperimentEncoder
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Encode mutant experiments
- encode(GeneRegulationSpecification, GeneRegulationDeterministicEncoder.HypotheticalRegulationPolicy) - Static method in class mx.unam.iimas.griffin.grn.code.MutantExperimentEncoder
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Encodes a mutant experiment
- encode(BooleanNetworkStateTrajectory, GeneRegulationSpecification, GeneRegulationDeterministicEncoder.HypotheticalRegulationPolicy) - Static method in class mx.unam.iimas.griffin.grn.code.StateTrajectoryEncoder
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Encodes the given trajectory
- encode(StateTransitionRule) - Static method in class mx.unam.iimas.griffin.grn.code.StateTransitionRuleEncoder
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Encodes the provided rule
- encode(StateTransitionRule, Set<Gene>) - Static method in class mx.unam.iimas.griffin.grn.code.StateTransitionRuleEncoder
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Encodes the provided rule
- encode(Set<BooleanNetworkState>, Map<Gene, Set<Gene>>) - Static method in class mx.unam.iimas.griffin.grn.code.SubspaceEncoder
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Encodes the input-output state pairs
- encodeConsistencyConstraint() - Method in class mx.unam.iimas.griffin.grn.code.analysis.KlarnerEncoder
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Encodes the consistency constraint (Mutual exclusion for complementary
literals)
- encodeImplicantConstraint() - Method in class mx.unam.iimas.griffin.grn.code.analysis.KlarnerEncoder
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Encodes the implicants constraints on the particular values of the
Boolean variables representing the vertices
- encodeProhibition(Set<BooleanNetworkState>, Map<Gene, Set<Gene>>) - Static method in class mx.unam.iimas.griffin.grn.code.FixedPointAttractorEncoder
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Encodes the prohibition for the set of states giving the provided
dependencies
- EncoderUtil - Class in mx.unam.iimas.griffin.grn.code
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Auxiliary class for encoding regulations
- EncoderUtil() - Constructor for class mx.unam.iimas.griffin.grn.code.EncoderUtil
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- encodeStabilityConstraint() - Method in class mx.unam.iimas.griffin.grn.code.analysis.KlarnerEncoder
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Encodes the stability constraint
- Epistasis - Interface in mx.unam.iimas.griffin.grn.models.epistasis
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Epistasis experiment
- Equality - Class in mx.unam.iimas.griffin.logic
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Logical equality or biconditional tree formula
- Equality(Formula, Formula) - Constructor for class mx.unam.iimas.griffin.logic.Equality
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Creates a biconditional or equality tree formula
- equals(Object) - Method in class mx.unam.iimas.griffin.graph.DirectedHypergraph.Vertex
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- equals(Object) - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkState
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- equals(Object) - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkStateTrajectory
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- equals(Object) - Method in class mx.unam.iimas.griffin.grn.Gene
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- equals(Object) - Method in class mx.unam.iimas.griffin.grn.GeneInteraction
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- equals(Object) - Method in class mx.unam.iimas.griffin.grn.GeneRegulation
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- equals(Object) - Method in class mx.unam.iimas.griffin.grn.GeneState
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- equals(Object) - Method in class mx.unam.iimas.griffin.grn.InputOutputStatePair
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- equals(Object) - Method in class mx.unam.iimas.griffin.grn.MutantExperiment
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- equals(Object) - Method in class mx.unam.iimas.griffin.grn.PartialBooleanNetworkState
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- equals(Object) - Method in class mx.unam.iimas.griffin.grn.SynchronousAttractorBasin
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- equals(Object) - Method in class mx.unam.iimas.griffin.logic.BooleanConstant
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- equals(Object) - Method in class mx.unam.iimas.griffin.logic.implicants.MintermMatching
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- equals(Object) - Method in class mx.unam.iimas.griffin.logic.Literal
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- equals(Object) - Method in class mx.unam.iimas.griffin.logic.Variable
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- equals(Object) - Method in class mx.unam.iimas.griffin.sat.PropositionalModel
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- evaluate(Formula, Interpretation) - Static method in class mx.unam.iimas.griffin.logic.util.FormulaEvaluator
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Evaluates the formula given the interpretation
- evaluate(int[][], boolean[]) - Static method in class mx.unam.iimas.griffin.logic.util.FormulaEvaluator
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Evaluates a formula in cnf-array-of-indices form
- ExactRegulationDeterministicEncoder - Class in mx.unam.iimas.griffin.grn.code
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Encodes gene regulation as a boolean expression
The encoding considers only the known regulators, hypothetical or any other
regulations are not allowed
- ExactRegulationDeterministicEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.ExactRegulationDeterministicEncoder
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- explicit() - Method in class mx.unam.iimas.griffin.grn.PartialBooleanNetworkState
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Obtains a set of all compatible states
- ExtendedRegulationDeterministicEncoder - Class in mx.unam.iimas.griffin.grn.code
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Encodes gene regulation as a boolean expression
The encoding considers not only the known regulators but also a hypothetical
set of regulators no other regulations besides these two types are allowed
- ExtendedRegulationDeterministicEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.ExtendedRegulationDeterministicEncoder
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- extractRegulation(Literal) - Static method in class mx.unam.iimas.griffin.grn.code.EncoderUtil
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Decodes the regulation from a given literal
- extractRegulations(PropositionalModel) - Static method in class mx.unam.iimas.griffin.grn.code.EncoderUtil
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Obtains the list of true regulations from a propositional model