- TARGET - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Name for capture group representing target gene
- ThieffryStableStates - Class in mx.unam.iimas.griffin.grn.util
-
SAT based Thieffry approach for finding stable states in a gene regulatory
network
- TIMEOUT - Static variable in class mx.unam.iimas.griffin.sat.ModelIterator
-
Timeout for the solver.
- toBDD(BooleanNetworkState) - Method in class mx.unam.iimas.griffin.grn.util.SteadyStateAnalyzer
-
Transform the provided into a BDD
- toCompactString(Set<GeneRegulation>) - Static method in class mx.unam.iimas.griffin.grn.explorer.topology.TopologyUtil
-
Compact representation of topology (Represents double regulations with
the '-&' symbols
- toListOfLiterals() - Method in class mx.unam.iimas.griffin.logic.Interpretation
-
Obtains the interpretation as a list of literals
- toMatrix(GeneRegulationSpecification, Set<Set<GeneRegulation>>) - Static method in class mx.unam.iimas.griffin.grn.explorer.topology.TopologyUtil
-
Represents the topologies as matrices
Rows are topologies Columns are edges, the order given by the order of
genes in the specification
- toOneAndZerosString(Comparator<? super GeneState>) - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkState
-
Returns a zeros and ones representation of the state using the provided
comparator to sort the genes
- TOPOLOGY_BLOCKER - Static variable in class mx.unam.iimas.griffin.grn.explorer.topology.StructureBlocker
-
The structure blocker for satisfying assignments
- TopologyIterator - Class in mx.unam.iimas.griffin.grn.explorer.topology
-
Generic topology iterator
- TopologyIterator(Set<GeneInteraction>) - Constructor for class mx.unam.iimas.griffin.grn.explorer.topology.TopologyIterator
-
- TopologyIteratorFilter - Interface in mx.unam.iimas.griffin.grn.explorer.topology
-
Filter for an Iterator of topologies
- TopologyIteratorType - Enum in mx.unam.iimas.griffin.grn.explorer.topology
-
Type of the topology iterator
- TopologyUtil - Class in mx.unam.iimas.griffin.grn.explorer.topology
-
General methods for manipulating topologies
- TopologyUtil() - Constructor for class mx.unam.iimas.griffin.grn.explorer.topology.TopologyUtil
-
- TopologyUtil - Class in mx.unam.iimas.griffin.grn.util
-
Utility functions for Topologies
- TopologyUtil() - Constructor for class mx.unam.iimas.griffin.grn.util.TopologyUtil
-
- TopologyVariant - Enum in mx.unam.iimas.griffin.grn.models.epistasis
-
Variants of topology
- toPrimeImplicant(SortedSet<Variable>, boolean) - Method in class mx.unam.iimas.griffin.logic.implicants.MintermMatching
-
The prime implicant for the matching
- toString(BDD) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
-
A string representation of the BDD
- toString() - Method in class mx.unam.iimas.griffin.bdd.QueryableAssignment
-
- toString() - Method in class mx.unam.iimas.griffin.graph.DirectedHypergraph.DirectedHyperEdge
-
- toString() - Method in class mx.unam.iimas.griffin.graph.DirectedHypergraph.Vertex
-
- toString() - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetwork
-
- toString() - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetworkInfo
-
- toString() - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkState
-
- toString() - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkStateTrajectory
-
- toString() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
- toString() - Method in class mx.unam.iimas.griffin.grn.explorer.io.AssignmentStatement
-
- toString() - Method in class mx.unam.iimas.griffin.grn.explorer.io.GeneListValue
-
- toString() - Method in class mx.unam.iimas.griffin.grn.explorer.util.GeneOrder
-
- toString() - Method in class mx.unam.iimas.griffin.grn.Gene
-
- toString() - Method in class mx.unam.iimas.griffin.grn.GeneInteraction
-
- toString() - Method in class mx.unam.iimas.griffin.grn.GeneRegulation
-
- toString() - Method in enum mx.unam.iimas.griffin.grn.GeneRegulation.Type
-
- toString() - Method in class mx.unam.iimas.griffin.grn.GeneState
-
- toString() - Method in class mx.unam.iimas.griffin.grn.InputOutputStatePair
-
- toString() - Method in class mx.unam.iimas.griffin.grn.MutantExperiment
-
- toString() - Method in class mx.unam.iimas.griffin.grn.PartialBooleanNetworkState
-
- toString() - Method in class mx.unam.iimas.griffin.grn.StateTransitionRule
-
- toString() - Method in class mx.unam.iimas.griffin.grn.util.NonDominanceTrapSetGraph
-
- toString() - Method in class mx.unam.iimas.griffin.logic.And
-
- toString() - Method in class mx.unam.iimas.griffin.logic.BooleanConstant
-
- toString() - Method in class mx.unam.iimas.griffin.logic.Equality
-
- toString() - Method in class mx.unam.iimas.griffin.logic.implicants.MintermMatching
-
- toString() - Method in class mx.unam.iimas.griffin.logic.implicants.MintermTable
-
- toString() - Method in class mx.unam.iimas.griffin.logic.implicants.PrimeImplicant
-
- toString() - Method in class mx.unam.iimas.griffin.logic.implicants.PrimeImplicantGraph
-
- toString() - Method in class mx.unam.iimas.griffin.logic.implicants.TruthTable
-
- toString() - Method in class mx.unam.iimas.griffin.logic.Implication
-
- toString() - Method in class mx.unam.iimas.griffin.logic.Interpretation
-
- toString() - Method in class mx.unam.iimas.griffin.logic.Literal
-
- toString() - Method in class mx.unam.iimas.griffin.logic.Not
-
- toString() - Method in class mx.unam.iimas.griffin.logic.Or
-
- toString() - Method in class mx.unam.iimas.griffin.logic.Variable
-
- toString() - Method in class mx.unam.iimas.griffin.sat.PropositionalModel
-
- toTermFormula() - Method in class mx.unam.iimas.griffin.logic.Interpretation
-
Obtains a term (conjunction of literals) representing the interpretation
- toTransitionTableString(StateTransitionRule) - Static method in class mx.unam.iimas.griffin.util.ModelPrinter
-
String representing the truth table for the given transition rule
- toTransitionTableString(Gene, Set<Gene>, PropositionalModel) - Static method in class mx.unam.iimas.griffin.util.ModelPrinter
-
String representation of truth table for the specified gene
Note: this function DOES NOT simplify the tables
Warning: The list of extended regulators should be the same as the one
used for encoding the search query, calling it with a different set (for
example the set of essential regulators) will result most likely in an
erroneous output.
- TrajectoriesValue - Class in mx.unam.iimas.griffin.grn.explorer.io
-
Value for state space trajectories
- TrajectoriesValue(String) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.TrajectoriesValue
-
Creates the value with the given input
- TransitionRelation - Class in mx.unam.iimas.griffin.grn.util
-
Asynchronous transition relation for a Boolean Network
- TransitionRelation() - Constructor for class mx.unam.iimas.griffin.grn.util.TransitionRelation
-
- TRUE - Static variable in class mx.unam.iimas.griffin.logic.BooleanConstant
-
True
- TruthTable - Class in mx.unam.iimas.griffin.logic.implicants
-
Truth table representation of a Boolean Function
- TruthTable(Formula) - Constructor for class mx.unam.iimas.griffin.logic.implicants.TruthTable
-
Creates the truth table for the given formula
- TruthTableParser - Class in mx.unam.iimas.griffin.grn.util
-
Parser for truth tables to DNF forms
- TruthTableParser() - Constructor for class mx.unam.iimas.griffin.grn.util.TruthTableParser
-
- TseitinCNFConverter - Class in mx.unam.iimas.griffin.sat
-
Converts a tree formula to CNF using Tseitin method
- TseitinCNFConverter(Formula) - Constructor for class mx.unam.iimas.griffin.sat.TseitinCNFConverter
-
Creates a converter for the given formula
- TypeGeneList - Class in mx.unam.iimas.griffin.grn.explorer.io
-
Encapsulates a list of genes
- TypeGeneList(String) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.TypeGeneList
-
Creates an instance of a gene list