G-Index

$ A B C D E F G H I K L M N O P Q R S T U V W Z

G

GENE - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp: Name for capture group representing a gene
Gene - Class in mx.unam.iimas.griffin.grn: Symbolic representation for a gene
Gene(String) - Constructor for class mx.unam.iimas.griffin.grn.Gene: Creates the gene
GeneInteraction - Class in mx.unam.iimas.griffin.grn: An interaction between genes
GeneInteraction(Gene, Gene, GeneInteractionType) - Constructor for class mx.unam.iimas.griffin.grn.GeneInteraction: Creates the interaction
GeneInteractionEncoder - Class in mx.unam.iimas.griffin.grn.code: Boolean sentence encoder for gene interactions
GeneInteractionEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.GeneInteractionEncoder
GeneInteractionListValue - Class in mx.unam.iimas.griffin.grn.explorer.io: List of gene regulations
GeneInteractionListValue(String) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.GeneInteractionListValue: Creates an instance of the class
GeneInteractionQueryEncoder - Class in mx.unam.iimas.griffin.grn.code: Encoder for gene interaction constraints
GeneInteractionQueryEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.GeneInteractionQueryEncoder
GeneInteractionType - Enum in mx.unam.iimas.griffin.grn: Types for describing interaction of genes
GeneListValue - Class in mx.unam.iimas.griffin.grn.explorer.io: Represents the list of genes
GeneListValue(String) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.GeneListValue: Value to set
GeneOrder - Class in mx.unam.iimas.griffin.grn.explorer.util: An ordering for the genes
GeneOrder(Map<Integer, Gene>) - Constructor for class mx.unam.iimas.griffin.grn.explorer.util.GeneOrder
GENERALIZED_INTERACTION - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp: Regular expression for generalized interactions
GeneralizedInteractionEncoder - Class in mx.unam.iimas.griffin.grn.code
GeneralizedInteractionEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.GeneralizedInteractionEncoder
GeneRegulation - Class in mx.unam.iimas.griffin.grn: A gene regulation is a relation between two genes that may be either positive or negative
GeneRegulation(Gene, Gene, GeneRegulation.Type) - Constructor for class mx.unam.iimas.griffin.grn.GeneRegulation: Creates a gene regulation between two genes
GeneRegulation.Type - Enum in mx.unam.iimas.griffin.grn: Types of regulatory interactions between two genes
GeneRegulationChecker - Class in mx.unam.iimas.griffin.grn.explorer.util: Utility class for checking regulation on GRNs
GeneRegulationChecker() - Constructor for class mx.unam.iimas.griffin.grn.explorer.util.GeneRegulationChecker
GeneRegulationDecoder - Interface in mx.unam.iimas.griffin.grn.code: Decodes models encoding Boolean networks satisfying regulatory constraints (@see GeneRegulationDeterministicEncoder)
GeneRegulationDeterministicDecoder - Class in mx.unam.iimas.griffin.grn.code: Decoder of boolean networks given models of a gene regulatory network encoding
GeneRegulationDeterministicDecoder(GeneRegulationSpecification) - Constructor for class mx.unam.iimas.griffin.grn.code.GeneRegulationDeterministicDecoder: Creates the decoder
GeneRegulationDeterministicEncoder - Class in mx.unam.iimas.griffin.grn.code: Encodes gene regulation as a boolean expression The encoding considers the active regulators in the specification, and according to the defined policy can also consider those that are hypothetical, outside these two cases no additional regulations are allowed
GeneRegulationDeterministicEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.GeneRegulationDeterministicEncoder: Creates the encoder
GeneRegulationDeterministicEncoder.HypotheticalRegulationPolicy - Enum in mx.unam.iimas.griffin.grn.code: How to treat hypothetical regulations in the encoding
GeneRegulationDeterministicEncoder.StableStatesPolicy - Enum in mx.unam.iimas.griffin.grn.code
GeneRegulationEncoder - Interface in mx.unam.iimas.griffin.grn.code: Encodes gene regulation specifications as boolean expressions
GeneRegulationFileParser - Class in mx.unam.iimas.griffin.grn.explorer.io: Parses a gene regulation specification
GeneRegulationFileParser() - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.GeneRegulationFileParser
GeneRegulationListValue - Class in mx.unam.iimas.griffin.grn.explorer.io: List of gene regulations
GeneRegulationListValue(String) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.GeneRegulationListValue: Creates an instance of the class
GeneRegulationQueryEncoder - Class in mx.unam.iimas.griffin.grn.code: Creates a boolean expression encoding for checking regulations in a GRN
GeneRegulationQueryEncoder(BooleanGeneRegulatoryNetwork) - Constructor for class mx.unam.iimas.griffin.grn.code.GeneRegulationQueryEncoder: Creates an encoder for the given network
GeneRegulationSpecification - Class in mx.unam.iimas.griffin.grn.explorer: A gene regulation specification is a set of known regulatory interactions as well as a set of hypothetical regulations.
GeneRegulationSpecification(Set<Gene>, Set<BooleanNetworkState>, Set<InputOutputStatePair>) - Constructor for class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Creates a gene regulation specification
GeneRegulationSpecification(Set<Gene>, Set<GeneRegulation>, Set<GeneRegulation>, Set<BooleanNetworkState>, Set<InputOutputStatePair>) - Constructor for class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Creates a gene regulation specification
GeneRegulationSpecification(Set<Gene>, Set<GeneRegulation>, Set<GeneRegulation>, Set<BooleanNetworkState>) - Constructor for class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Creates a gene regulation specification
GeneState - Class in mx.unam.iimas.griffin.grn: The state of a particular gene
GeneState(Gene, Boolean) - Constructor for class mx.unam.iimas.griffin.grn.GeneState: Creates the state for the gene
GeneUtil - Class in mx.unam.iimas.griffin.grn.util: Utility class for genes
GeneUtil() - Constructor for class mx.unam.iimas.griffin.grn.util.GeneUtil
get(String) - Method in class mx.unam.iimas.griffin.bdd.BDDModule: Obtains the BDD with the provided name
get(int) - Method in class mx.unam.iimas.griffin.bdd.BDDModule: Obtains the BDD with the provided id
get(String) - Method in class mx.unam.iimas.griffin.grn.explorer.Parameters: Obtains the message for the given key
getActiveInteractions(GeneRegulationSpecification) - Static method in class mx.unam.iimas.griffin.grn.code.GeneralizedInteractionEncoder: Obtains the active interactions
getAll() - Method in class mx.unam.iimas.griffin.grn.explorer.topology.InteractionClassifier: Obtains the set of all interactions
getAllAdjacentStates() - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkState: Obtains all adjacent states Two states are adjacent if their Hamming distance equals one (they differ in the state of exactly one gene)
getAllMinterms() - Method in class mx.unam.iimas.griffin.logic.implicants.MintermTable: Obtains all minterms of the table
getArity() - Method in enum mx.unam.iimas.griffin.logic.Operator: Number of arguments of the operation
getAsterisks() - Method in class mx.unam.iimas.griffin.grn.PartialBooleanNetworkState: Obtains the set of unknown genes
getAttractor() - Method in class mx.unam.iimas.griffin.grn.SynchronousAttractorBasin: Obtains the Boolean network state trajectory representing the synchronous attractor
getAttractorBDD() - Method in class mx.unam.iimas.griffin.grn.SynchronousAttractorBasin: Obtains the attractor as a BDD representing the states in the attractor
getAttractors() - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetworkInfo: Obtains the set of attractors for the Boolean network
getAttractors() - Method in class mx.unam.iimas.griffin.grn.util.SynchronousSteadyStateAnalyzer: Obtains the set of all attractors
getBackwardMap(BooleanGeneRegulatoryNetwork) - Static method in class mx.unam.iimas.griffin.grn.util.TransitionRelation: Obtains the Map that relates all prime variables (next time) with their corresponding variables (present time)
getBasin() - Method in class mx.unam.iimas.griffin.grn.SynchronousAttractorBasin: Obtains the basin of attraction as a BDD representing the states in the basin of attraction
getBasins() - Method in class mx.unam.iimas.griffin.grn.util.SynchronousSteadyStateAnalyzer: Obtains the list of Basins of attraction for the Boolean network Basins of attraction include their attractors
getBDDModule() - Method in class mx.unam.iimas.griffin.grn.util.SteadyStateAnalyzer: Obtains the BDD module of this class
getBooleanConstant(BooleanConstant) - Method in class mx.unam.iimas.griffin.bdd.BDDModule: Obtains the BDD representing the Boolean constant
getCardinality() - Method in class mx.unam.iimas.griffin.math.Combinations: Total number of combinations
getCNFFormulaAsArray() - Method in interface mx.unam.iimas.griffin.sat.CNFConverter: Obtains the CNF representation of the formula as an array of integers The CNF is simply an array of clauses, a clause is an array of literals a literal is simply a positive or a negative integer, a positive number n represents the n-th propositional variable a negative number n represents the negation of the n-th propositional variable
getCNFFormulaAsArray() - Method in class mx.unam.iimas.griffin.sat.TseitinCNFConverter
getCNFFormulaTree() - Method in interface mx.unam.iimas.griffin.sat.CNFConverter: Obtains the CNF formula as a tree
getCNFFormulaTree() - Method in class mx.unam.iimas.griffin.sat.TseitinCNFConverter
getCodingMap() - Method in interface mx.unam.iimas.griffin.sat.CNFConverter: Obtains the coding map that relates the original variables to their index in CNF array of indices representation
getCodingMap() - Method in class mx.unam.iimas.griffin.sat.TseitinCNFConverter
getCore() - Method in class mx.unam.iimas.griffin.grn.explorer.topology.InteractionClassifier: Obtains the list of gene interactions that are mandatory and completely defined
getCountClasses() - Method in class mx.unam.iimas.griffin.logic.implicants.MintermTable: Obtains the count classes for the minterm table The count classes is a list of lists containing the minterm indices having a given number of ones in their boolean representation.
getCurrentCount() - Method in class mx.unam.iimas.griffin.grn.explorer.topology.StructureIterator: Obtains the number of models found so far
getCurrentCount() - Method in interface mx.unam.iimas.griffin.sat.AllSATSolver: Obtains the number of models found so far
getCurrentCount() - Method in class mx.unam.iimas.griffin.sat.ModelIterator
getCurrentId() - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser: the current Id of the network in the iteration
getCurrentNetwork() - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser: the current network in the iteration
getCurrentTopology() - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser: the current topology in the iteration
getCycles() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the allowed cyclic attractors
getDecodingMap() - Method in interface mx.unam.iimas.griffin.sat.CNFConverter: Obtains the decoding map that relates the indices in the CNF array of indices representation to the variables in the formula
getDecodingMap() - Method in class mx.unam.iimas.griffin.sat.TseitinCNFConverter
getDependencies() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the set of dependencies
getDependencies(GeneRegulationDeterministicEncoder.HypotheticalRegulationPolicy) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the dependencies map according to provided policy
getEdge(Variable) - Method in class mx.unam.iimas.griffin.grn.code.analysis.KlarnerEncoder: Obtains the Edge represented by the given variable
getEdges() - Method in class mx.unam.iimas.griffin.graph.DirectedHypergraph: Obtains the set of directed hyperedges
getEncodedRowVariableName(Gene, int) - Static method in class mx.unam.iimas.griffin.grn.code.EncoderUtil: Obtains the variable encoding for the given gene and row
getExtendedRegulators(Gene) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtain the extended regulators of the specified gene Extended meaning known and hypothetical regulations are taking into account
getFalseIndices() - Method in class mx.unam.iimas.griffin.logic.implicants.TruthTable: Obtains the indices of the rows evaluating to false
getFixPointAttractors() - Method in class mx.unam.iimas.griffin.grn.util.SteadyStateAnalyzer: Obtains the set of fix points attractors
getFormula() - Method in class mx.unam.iimas.griffin.grn.code.StableStatesFormulaPair: Obtains the encoding for stable states constraint
getFormula() - Method in class mx.unam.iimas.griffin.logic.implicants.TruthTable: Obtains the Boolean expression for the truth table
getForwardMap(BooleanGeneRegulatoryNetwork) - Static method in class mx.unam.iimas.griffin.grn.util.TransitionRelation: Obtains the Map that relates all variables to their prime versions (next time variables)
getGene() - Method in class mx.unam.iimas.griffin.grn.GeneState: The gene
getGene() - Method in class mx.unam.iimas.griffin.grn.StateTransitionRule: Obtains the gene of the transition
getGeneAtPosition(Integer) - Method in class mx.unam.iimas.griffin.grn.explorer.util.GeneOrder: Obtains the gene at the provided position
getGeneInteractions() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the set of all interactions
getGeneOf() - Method in class mx.unam.iimas.griffin.grn.explorer.io.GeneListValue: Obtains the index to gene map
getGeneOrdering() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the ordering of the genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetwork: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.explorer.io.GeneListValue: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.ArabidopsisThalianaFlowerDevelopment: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaBMC2010Reference: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel01: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel02: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel03: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel04: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel05: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel06: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel07: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel08: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel09: Obtains the set of genes
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel10: Obtains the set of genes
getGenes() - Method in interface mx.unam.iimas.griffin.grn.models.epistasis.Epistasis
getGenes() - Method in class mx.unam.iimas.griffin.grn.models.epistasis.Motif
getGeneState(Gene) - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkState: Whether the gene is expressed or not
getGeneState() - Method in class mx.unam.iimas.griffin.grn.MutantExperiment: Obtains the gene states for the mutant
getGeneVariables() - Method in class mx.unam.iimas.griffin.grn.util.BDDBooleanNetworkModule: Obtains the propositional variables representing the genes
getHead() - Method in class mx.unam.iimas.griffin.graph.DirectedHypergraph.DirectedHyperEdge: Obtains the head of the hyperedge
getHypotheticalRegulations() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the set of hypothetical regulations
getHypotheticalRegulations(Gene) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the hypothetical regulations of the given gene
getID(String) - Method in class mx.unam.iimas.griffin.bdd.BDDModule: Obtains the ID for the provided BDD name
getIDLastTopology() - Method in class mx.unam.iimas.griffin.grn.explorer.topology.SequentialTopologyIterator: Returns the ID of the last retrieved topology
getIds() - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser: Get the list of identifiers for the networks
getImpliedValue() - Method in class mx.unam.iimas.griffin.logic.implicants.PrimeImplicant: True when the implied value is true
getIncomingEdges(DirectedHypergraph<T>.Vertex) - Method in class mx.unam.iimas.griffin.graph.DirectedHypergraph: Obtains the set of all incoming edges for the given vertices
getInput() - Method in class mx.unam.iimas.griffin.grn.InputOutputStatePair: Obtains the input
getInputOutputPairs() - Method in class mx.unam.iimas.griffin.grn.explorer.io.InputOutputPairsValue: Obtains the parsed input-output pairs
getInputOutputStatePairs() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the input-output pairs
getInstance(Formula...) - Method in enum mx.unam.iimas.griffin.logic.Operator: Obtains a formula for operating the provided arguments
getInstance() - Static method in class mx.unam.iimas.griffin.sat.AllSAT4j: Obtains a reference to the solver
getInteractions() - Method in class mx.unam.iimas.griffin.grn.explorer.io.GeneInteractionListValue: Obtains the set of generalized gene interactions
getInteractions(Set<GeneRegulation>) - Static method in class mx.unam.iimas.griffin.grn.GeneInteraction: Obtains the set of interactions from the set of regulations
getInteractions() - Method in interface mx.unam.iimas.griffin.grn.models.epistasis.Epistasis
getInteractions() - Method in class mx.unam.iimas.griffin.grn.models.epistasis.Motif
getInteractionsOfGene(Gene) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the interactions
getKey() - Method in enum mx.unam.iimas.griffin.grn.explorer.io.AssignmentType: the key for the assignment (left hand side)
getKeyword() - Method in enum mx.unam.iimas.griffin.grn.explorer.topology.TopologyIteratorType: obtains the keyword of the iterator type
getKnownRegulations() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the set of known regulations
getKnownRegulations(Gene) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the regulations of the given gene
getKnownRegulators(Gene) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtain the known regulators of the given gene
getLeft() - Method in class mx.unam.iimas.griffin.grn.explorer.io.AssignmentStatement: Obtains the left side of the assignment
getLeftSubformula() - Method in class mx.unam.iimas.griffin.logic.BinaryFormula
getLeftSubformula() - Method in interface mx.unam.iimas.griffin.logic.BinaryOperation: Obtains the left sub-formula tree
getLength() - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkStateTrajectory: Obtains the length of the trajectory (number of different states)
getLimitToNumberOfNetworks() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the limit to the number of networks to explore -1 means no limit
getLiteral(Variable) - Method in class mx.unam.iimas.griffin.sat.PropositionalModel: Obtains the literal for the given variable
getLiterals() - Method in class mx.unam.iimas.griffin.sat.PropositionalModel: Obtains the literals that represent the model
getLiteralsOfEncoding(InputOutputStatePair, Map<Gene, Set<Gene>>) - Static method in class mx.unam.iimas.griffin.grn.code.InputOutputEncoder: Obtains the Literals used for encoding the input-output pair
getMaximum() - Method in class mx.unam.iimas.griffin.math.Interval: Obtains the maximum value of the interval
getMinimum() - Method in class mx.unam.iimas.griffin.math.Interval: Obtains the minimum value of the interval
getMintermsCount() - Method in class mx.unam.iimas.griffin.logic.implicants.MintermTable: Total number of minterms in the table
getMutantExperiment() - Method in class mx.unam.iimas.griffin.grn.explorer.io.MutantExperimentSetValue: Obtains the mutant experiment
getMutantExperiments() - Method in interface mx.unam.iimas.griffin.grn.models.epistasis.Epistasis
getMutantExperiments() - Method in class mx.unam.iimas.griffin.grn.models.epistasis.Motif
getMutants() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the mutant experiments of the specification ¡
getMutants() - Method in class mx.unam.iimas.griffin.grn.models.Ejemplo3Genes: Obtains the mutants for the example
getName() - Method in class mx.unam.iimas.griffin.grn.Gene: the name of the gene
getName() - Method in enum mx.unam.iimas.griffin.logic.Operator: The name of the operation
getName() - Method in class mx.unam.iimas.griffin.logic.Variable: Obtains the name of the variable
getNegativeFormula() - Method in class mx.unam.iimas.griffin.grn.code.RegulationFormulaPair: Obtains the definition formula for the negative regulation
getNegativeRegulationVariable() - Method in class mx.unam.iimas.griffin.grn.code.RegulationFormulaPair: Obtains the variable encoding the negative regulation
getNegativeStates() - Method in class mx.unam.iimas.griffin.grn.explorer.io.BooleanNetworkStateSetValue: Obtains the set of all negative Boolean network states
getNegativeStatesAsList() - Method in class mx.unam.iimas.griffin.grn.explorer.io.BooleanNetworkStateSetValue: Obtains the list of negative states in the order of parsing
getNetwork() - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetworkInfo: Obtains the gene variables and update rules describing the Boolean network
getNetwork() - Method in class mx.unam.iimas.griffin.grn.util.BDDBooleanNetworkModule: Obtains the Boolean Network
getNetworks() - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser: Obtains the list of Boolean networks
getNewSmallSolver() - Method in class mx.unam.iimas.griffin.sat.AllSAT4j: Obtains the All-SAT Solver suitable for small instances of SAT problems
getNotStableStatesFormula() - Method in class mx.unam.iimas.griffin.grn.code.StableStatesFormulaPair
getNumberOfCycles() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the number of cycles
getNumberOfGenes() - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkState: The number of genes in the state
getNumberOfGenes() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: The number of genes in the network
getOpposite(DirectedHypergraph<Literal>.Vertex) - Method in class mx.unam.iimas.griffin.logic.implicants.PrimeImplicantGraph: Returns the opposite vertex to the given vertex two vertices are opposite to one another if they represent complementary literals
getOutgoingEdges(DirectedHypergraph<T>.Vertex) - Method in class mx.unam.iimas.griffin.graph.DirectedHypergraph: Obtains the set of all outgoing edges for the given vertices
getOutput() - Method in class mx.unam.iimas.griffin.grn.InputOutputStatePair: Obtains the output
getOutputFile() - Method in class mx.unam.iimas.griffin.grn.explorer.Griffin: obtains the name of the output file
getOutputFileNames() - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser: Obtains the list of file names
getPositionOfGene(Gene) - Method in class mx.unam.iimas.griffin.grn.explorer.util.GeneOrder: Obtains the position of the given gene
getPositiveFormula() - Method in class mx.unam.iimas.griffin.grn.code.RegulationFormulaPair: Obtains the definition formula for the positive regulation
getPositiveRegulationVariable() - Method in class mx.unam.iimas.griffin.grn.code.RegulationFormulaPair: obtains the variable encoding the positive regulation
getPositiveStates() - Method in class mx.unam.iimas.griffin.grn.explorer.io.BooleanNetworkStateSetValue: Obtains the set of all positive Boolean network states
getPositiveStatesAsList() - Method in class mx.unam.iimas.griffin.grn.explorer.io.BooleanNetworkStateSetValue: Obtains the list of positive states in the order of parsing
getPossibleRegulations(GeneInteractionType) - Static method in class mx.unam.iimas.griffin.grn.explorer.topology.TopologyIterator: Obtains the list of possible regulations for a given gene interaction type
getPrimeImplicants() - Method in class mx.unam.iimas.griffin.logic.implicants.AdjacencyTable: The list of prime implicants
getProhibitedStableStates() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the set of prohibited stable states
getQueryFile() - Method in class mx.unam.iimas.griffin.grn.explorer.Griffin: obtains the name of the query file
getRegulations() - Method in class mx.unam.iimas.griffin.grn.explorer.io.GeneRegulationListValue: Obtains the set of gene regulations
getRegulationVariableName(Gene, Gene, GeneRegulation.Type) - Static method in class mx.unam.iimas.griffin.grn.code.EncoderUtil: Obtains the variable encoding the positive regulation for the given genes
getRight() - Method in class mx.unam.iimas.griffin.grn.explorer.io.AssignmentStatement: Obtains the right side of the assignment
getRightSubformula() - Method in class mx.unam.iimas.griffin.logic.BinaryFormula
getRightSubformula() - Method in interface mx.unam.iimas.griffin.logic.BinaryOperation: Obtains the right sub-formula tree
getSetOfAttractors(BooleanGeneRegulatoryNetwork) - Method in class mx.unam.iimas.griffin.grn.explorer.attractor.AttractorSetIterator: Obtains the set of attractors of the network
getSingleFormula(Set<GeneInteraction>, Map<Gene, Set<Gene>>, GeneRegulationDeterministicEncoder.StableStatesPolicy, GeneRegulationSpecification) - Static method in class mx.unam.iimas.griffin.grn.code.GeneralizedInteractionEncoder: Obtains the encoding formula for the given parameters
getSingleFormula(Set<GeneInteraction>, Map<Gene, Set<Gene>>, GeneRegulationSpecification) - Static method in class mx.unam.iimas.griffin.grn.code.GeneralizedInteractionEncoder: Obtains a single formula for the given experiment
getSingleFormula(GeneRegulationSpecification) - Static method in class mx.unam.iimas.griffin.grn.code.GeneralizedInteractionEncoder: Obtains a single formula for the given experiment
getSolver() - Method in class mx.unam.iimas.griffin.grn.util.DubrovaAttractors: The model iterator
getSolver() - Method in class mx.unam.iimas.griffin.sat.AllSAT4j: Obtains the All-SAT Solver
getSource() - Method in interface mx.unam.iimas.griffin.grn.Dependency: Obtains the independent agent
getSource() - Method in class mx.unam.iimas.griffin.grn.GeneInteraction: the source of the interaction
getSource() - Method in class mx.unam.iimas.griffin.grn.GeneRegulation: The source of the regulation (gene that regulates)
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.ArabidopsisThalianaFlowerDevelopment: Obtains the stable states for the network
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaBMC2010Reference: Obtains the stable states for the network
getStable(Set<Gene>) - Method in interface mx.unam.iimas.griffin.grn.models.AzpeitiaModel
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel01: Obtains the stable states for the network
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel02: Obtains the stable states for the network
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel03: Obtains the stable states for the network
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel04: Obtains the stable states for the network
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel05: Obtains the stable states for the network
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel06: Obtains the stable states for the network
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel07: Obtains the stable states for the network
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel08: Obtains the stable states for the network
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel09: Obtains the stable states for the network
getStable(Set<Gene>) - Method in class mx.unam.iimas.griffin.grn.models.AzpeitiaModel10: Obtains the stable states for the network
getStable() - Method in interface mx.unam.iimas.griffin.grn.models.epistasis.Epistasis
getStable() - Method in class mx.unam.iimas.griffin.grn.models.epistasis.Motif
getStableStates() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the set of stable states
getStableStates() - Method in class mx.unam.iimas.griffin.grn.MutantExperiment: Obtains the set of stable states for the mutant
getStableStates(BooleanGeneRegulatoryNetwork) - Static method in class mx.unam.iimas.griffin.grn.util.ThieffryStableStates: Obtains the stable states for the boolean gene regulatory network
getStableStatesFormula() - Method in class mx.unam.iimas.griffin.grn.code.StableStatesFormulaPair
getState() - Method in class mx.unam.iimas.griffin.grn.GeneState: Whether the gene is expressed or not
getStateAsList() - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkState: Obtains the state as a list of gene states
getStateTransitionRules() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the set of known state transition rules
getStateTransitionRules() - Method in class mx.unam.iimas.griffin.grn.explorer.io.UpdateRulesValue: Obtains the state transition rules
getSubformula() - Method in class mx.unam.iimas.griffin.logic.Not: Obtains the tree subformula
getSubformula() - Method in interface mx.unam.iimas.griffin.logic.UnaryOperation: Obtains the sub-formula tree
getSubspaces() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the set of subspaces
getSymbol() - Method in enum mx.unam.iimas.griffin.grn.GeneRegulation.Type: Obtains the symbol representing the regulation
getSymbol() - Method in enum mx.unam.iimas.griffin.logic.Operator: The symbol(s) use to represent the operation
getTail() - Method in class mx.unam.iimas.griffin.graph.DirectedHypergraph.DirectedHyperEdge: Obtains the tail of the hyperedge
getTarget() - Method in interface mx.unam.iimas.griffin.grn.Dependency: Obtains the dependent agent
getTarget() - Method in class mx.unam.iimas.griffin.grn.GeneInteraction: the target of the interaction
getTarget() - Method in class mx.unam.iimas.griffin.grn.GeneRegulation: The target of the regulation (gene that is regulated)
getTopologicalDistanceRadius() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the topological distance exploration radius for the radial iterator
getTopologies() - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser: Obtains the list of topologies or network structures
getTopology() - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetworkInfo: Obtains the topology of the network
getTopologyIteratorType() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the type of the topology iterator
getTopologyRange() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification: Obtains the range of topologies to explore
getTotalNumberOfTopologies() - Method in class mx.unam.iimas.griffin.grn.explorer.topology.SequentialTopologyIterator: Obtains the total number of topologies
getTrajectory() - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkStateTrajectory: Obtains the trajectory as input-output pairs
getTransitionFormula() - Method in class mx.unam.iimas.griffin.grn.StateTransitionRule: Obtains the transition boolean formula
getTransitionRelation() - Method in class mx.unam.iimas.griffin.grn.util.SteadyStateAnalyzer: Obtains the BDD representing the asynchronous transition relation
getTransitionRuleOf(Gene) - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetwork: Obtains the transition rule of the provided gene
getTransitionRules() - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetwork: Obtains the state transition rules
getTrueIndices() - Method in class mx.unam.iimas.griffin.logic.implicants.TruthTable: Obtains the indices of the rows evaluating to true
getTruthTable() - Method in class mx.unam.iimas.griffin.logic.implicants.MintermTable: Returns the truth table
getType() - Method in class mx.unam.iimas.griffin.grn.GeneInteraction: the type of the interaction
getType() - Method in enum mx.unam.iimas.griffin.grn.GeneInteractionType: Obtains the type of the interaction
getType() - Method in class mx.unam.iimas.griffin.grn.GeneRegulation: The type of regulation
getValue() - Method in class mx.unam.iimas.griffin.graph.DirectedHypergraph.Vertex: Obtains the value of the vertex
getValue() - Method in class mx.unam.iimas.griffin.logic.BooleanConstant: Obtains the constant value
getValueOf(Variable) - Method in class mx.unam.iimas.griffin.bdd.QueryableAssignment: Obtains the boolean value of the given variable
getValues() - Method in class mx.unam.iimas.griffin.logic.implicants.TruthTable: Obtains the values of all rows in the table
getVariable() - Method in class mx.unam.iimas.griffin.grn.explorer.topology.InteractionClassifier: Obtains the list of gene interactions that are variable (can take one of many values)
getVariable() - Method in class mx.unam.iimas.griffin.logic.Literal: Obtains the propositional variable
getVariableMandatory() - Method in class mx.unam.iimas.griffin.grn.explorer.topology.InteractionClassifier: Obtains the list of variable interactions that are mandatory (they cannot be missing)
getVariableOptional() - Method in class mx.unam.iimas.griffin.grn.explorer.topology.InteractionClassifier: Obtains the list of gene interactions that can take one of many values, one of them the no regulation
getVariables() - Method in class mx.unam.iimas.griffin.bdd.QueryableAssignment: Obtain the set of variables
getVariables() - Method in class mx.unam.iimas.griffin.logic.implicants.TruthTable: Obtains the set of Boolean Variables
getVertex(Variable) - Method in class mx.unam.iimas.griffin.grn.code.analysis.KlarnerEncoder: Obtains the vertex represented by the given variable
getVertices() - Method in class mx.unam.iimas.griffin.graph.DirectedHypergraph: Obtains the set of vertices
Griffin - Class in mx.unam.iimas.griffin.grn.explorer: Gene Regulatory Interaction Formulator For Inquiring Networks
Griffin() - Constructor for class mx.unam.iimas.griffin.grn.explorer.Griffin: Creates a searcher class
GriffinBackup - Class in mx.unam.iimas.griffin.grn.explorer: Gene Regulatory Interaction Formulator For Inquiring Networks
GriffinBackup() - Constructor for class mx.unam.iimas.griffin.grn.explorer.GriffinBackup: Creates a searcher class

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