- addAsteriskGene(Gene) - Method in class mx.unam.iimas.griffin.grn.PartialBooleanNetworkState
-
Adds a gene of unknown state
- addMutantExperiment(MutantExperiment) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Adds a mutant experiment
- addStateTransitionRules(StateTransitionRule) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Adds a state transition rule
- AdjacencyTable - Class in mx.unam.iimas.griffin.logic.implicants
-
Adjacency table for n-th order differences
- AdjacencyTable(MintermTable) - Constructor for class mx.unam.iimas.griffin.logic.implicants.AdjacencyTable
-
Creates the table of adjacencies providing the minterm table
- AdjacencyTable(AdjacencyTable, int) - Constructor for class mx.unam.iimas.griffin.logic.implicants.AdjacencyTable
-
Creates the table of adjacencies providing the previous order table
- ALL - Static variable in enum mx.unam.iimas.griffin.logic.Operator
-
List of all supported operations
- AllSAT4j - Class in mx.unam.iimas.griffin.sat
-
Wrapper for using sat4j incremental solver
- AllSATSolver - Interface in mx.unam.iimas.griffin.sat
-
Finds all models of a sentence
- allStructures() - Method in class mx.unam.iimas.griffin.grn.explorer.topology.StructureIterator
-
Obtains the set of all satisfying structures
- And - Class in mx.unam.iimas.griffin.logic
-
And tree formula
- And(Formula, Formula) - Constructor for class mx.unam.iimas.griffin.logic.And
-
Creates the and tree formula
- ArabidopsisThalianaFlowerDevelopment - Class in mx.unam.iimas.griffin.grn.models
-
- ArabidopsisThalianaFlowerDevelopment() - Constructor for class mx.unam.iimas.griffin.grn.models.ArabidopsisThalianaFlowerDevelopment
-
Creates an instance of the model
- ArabidopsisThalianaFlowerDevelopmentSpecification - Class in mx.unam.iimas.griffin.grn.models
-
- ArabidopsisThalianaFlowerDevelopmentSpecification() - Constructor for class mx.unam.iimas.griffin.grn.models.ArabidopsisThalianaFlowerDevelopmentSpecification
-
Creates the gene regulation specification
- areThereCyclicAttractors() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Queries whether there are cyclic attractors in the specification
- areThereInputOutputPairs() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Queries the existence of input-output pairs in the specification
- areThereInteractions() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Whether or not there are generalized gene interactions in the
specification
- areThereMutantExperiments() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Mutant experimental evidence
- areThereSubspaces() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Queries the existence of subspaces
- areThereTransitionRules() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
If there are any known update rules to consider
- asArray(StateTransitionRule, Set<Variable>) - Static method in class mx.unam.iimas.griffin.util.ModelPrinter
-
Obtains the Boolean function as an array of booleans
- asArray(StateTransitionRule, List<Variable>) - Static method in class mx.unam.iimas.griffin.util.ModelPrinter
-
Obtains the Boolean function as an array of booleans
- asBDD(Variable) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
-
Transforms the provided variable returning the corresponding BDD
- asFormula(BDD) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
-
Transforms the bdd to a tree formula
- asFormula() - Method in class mx.unam.iimas.griffin.logic.implicants.PrimeImplicant
-
the implicant as a tree formula
- asFormula() - Method in class mx.unam.iimas.griffin.logic.Literal
-
Obtains the literal as a tree formula
- asFormula(Variable, boolean) - Static method in class mx.unam.iimas.griffin.logic.Literal
-
returns a tree formula for the literal corresponding to the given
variable and value
- asGenes(Set<Variable>) - Static method in class mx.unam.iimas.griffin.grn.util.GeneUtil
-
Return the set Genes represented by the given variables
- asInteger() - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkState
-
the boolean state as an integer (Binary based 2 positional
representation)
- asInteraction(Gene, Gene, TopologyIterator.PossibleRegulation) - Static method in class mx.unam.iimas.griffin.grn.explorer.topology.TopologyIterator
-
Obtains a gene interaction compatible with the provided type
- asLiterals() - Method in class mx.unam.iimas.griffin.logic.implicants.PrimeImplicant
-
the implicant as a list of literals
- asRegulations(Gene, Gene, TopologyIterator.PossibleRegulation) - Static method in class mx.unam.iimas.griffin.grn.explorer.topology.TopologyIterator
-
Obtains the set of all possible regulations described by the type of
interaction
- assign(Variable, boolean) - Method in class mx.unam.iimas.griffin.logic.Interpretation
-
Assigns the value to the specified variable
- ASSIGNMENT_STATEMENT - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Regular expression matching an assignment statement
- AssignmentStatement - Class in mx.unam.iimas.griffin.grn.explorer.io
-
An assignment statement for a gene regulation file specification
- AssignmentStatement() - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.AssignmentStatement
-
- AssignmentType - Enum in mx.unam.iimas.griffin.grn.explorer.io
-
The assignment types for the specification
- AssignmentValue - Class in mx.unam.iimas.griffin.grn.explorer.io
-
Value for an specification assignment
- AssignmentValue(String) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.AssignmentValue
-
Creates an instance of the value for the assignment
- asStringOfOnesAndZeros(StateTransitionRule, GeneOrder) - Static method in class mx.unam.iimas.griffin.util.ModelPrinter
-
Obtains a boolean array with the values of the truth table considering
alphabetical order in a String representation
- ASTERISK - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Asterisk
- AsynchronousSteadyStateAnalyzer - Class in mx.unam.iimas.griffin.grn.util
-
Analyzes steady state behavior of boolean networks
- AsynchronousSteadyStateAnalyzer(BooleanGeneRegulatoryNetwork) - Constructor for class mx.unam.iimas.griffin.grn.util.AsynchronousSteadyStateAnalyzer
-
Creates the analyzer for the given network
- AsynchronousSteadyStateAnalyzer(BooleanGeneRegulatoryNetwork, BDDModule) - Constructor for class mx.unam.iimas.griffin.grn.util.AsynchronousSteadyStateAnalyzer
-
- AsynchronousTransitionRelation - Class in mx.unam.iimas.griffin.grn.util
-
Asynchronous transition relation for a Boolean Network
- AsynchronousTransitionRelation() - Constructor for class mx.unam.iimas.griffin.grn.util.AsynchronousTransitionRelation
-
- AttractorSetExplorer - Class in mx.unam.iimas.griffin.grn.explorer
-
Explorer of sets of attractors compatible with biological constraints
- AttractorSetExplorer() - Constructor for class mx.unam.iimas.griffin.grn.explorer.AttractorSetExplorer
-
- AttractorSetIterator - Class in mx.unam.iimas.griffin.grn.explorer.attractor
-
Iterator over the set of all sets of attractors
- AttractorSetIterator(GeneRegulationSpecification) - Constructor for class mx.unam.iimas.griffin.grn.explorer.attractor.AttractorSetIterator
-
Creates the iterator
- AttractorUtil - Class in mx.unam.iimas.griffin.grn.explorer.attractor
-
Utility methods for attractors
- AttractorUtil() - Constructor for class mx.unam.iimas.griffin.grn.explorer.attractor.AttractorUtil
-
- AzpeitiaBMC2010Reference - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaBMC2010Reference() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaBMC2010Reference
-
Creates an instance of model 2
- AzpeitiaModel - Interface in mx.unam.iimas.griffin.grn.models
-
- AzpeitiaModel01 - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaModel01() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaModel01
-
Creates an instance of model 2
- AzpeitiaModel02 - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaModel02() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaModel02
-
Creates an instance of model 2
- AzpeitiaModel03 - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaModel03() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaModel03
-
Creates an instance of model 3
- AzpeitiaModel04 - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaModel04() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaModel04
-
Creates an instance of model 4
- AzpeitiaModel05 - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaModel05() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaModel05
-
Creates an instance of model 5
- AzpeitiaModel06 - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaModel06() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaModel06
-
Creates an instance of model 6
- AzpeitiaModel07 - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaModel07() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaModel07
-
Creates an instance of model 7
- AzpeitiaModel08 - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaModel08() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaModel08
-
Creates an instance of model 8
- AzpeitiaModel09 - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaModel09() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaModel09
-
Creates an instance of model 9
- AzpeitiaModel10 - Class in mx.unam.iimas.griffin.grn.models
-
Azpeitia, E., Weinstein, N., Benítez, M., Mendoza, L., and Alvarez-Buylla, E.
- AzpeitiaModel10() - Constructor for class mx.unam.iimas.griffin.grn.models.AzpeitiaModel10
-
Creates an instance of model 10