- decode(PropositionalModel) - Method in interface mx.unam.iimas.griffin.grn.code.GeneRegulationDecoder
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Decodes a model as a Boolean network
- decode(PropositionalModel) - Method in class mx.unam.iimas.griffin.grn.code.GeneRegulationDeterministicDecoder
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- decode(PropositionalModel, Set<Gene>, Map<Gene, Set<Gene>>) - Static method in class mx.unam.iimas.griffin.grn.code.GeneRegulationDeterministicDecoder
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Decodes the propositional model using given gene dependencies map
This class detects fictitious regulators and leave them out of the
disjunctive normal form
- decode(GeneRegulationSpecification, PropositionalModel) - Static method in class mx.unam.iimas.griffin.util.ModelDecoder
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Decodes a gene regulatory network from a propositional model
- decode(Set<Gene>, int) - Static method in class mx.unam.iimas.griffin.util.StateUtil
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Decodes the network state given an integer
- decodeID(Integer) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
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Obtains the name for the given id
- decodeTrapSet(PropositionalModel, KlarnerEncoder, BDDModule) - Static method in class mx.unam.iimas.griffin.grn.code.analysis.KlarnerDecoder
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Decodes the propositional model to a trap set represented by a Binary
Decision Diagram
- DefaultModelBlocker - Class in mx.unam.iimas.griffin.sat
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This class blocks every model found considering only relevant variables
(doesn't block switching variables, therefore getting rid of uninteresting
solutions)
- DefaultModelBlocker() - Constructor for class mx.unam.iimas.griffin.sat.DefaultModelBlocker
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- Dependency<T> - Interface in mx.unam.iimas.griffin.grn
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Dependency among two entities
- DetailedNetworkWriter - Class in mx.unam.iimas.griffin.grn.explorer.io
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Detailed network file writer
- DetailedNetworkWriter(String) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.DetailedNetworkWriter
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Creates the writer
- DirectedHyperEdge(Set<DirectedHypergraph<T>.Vertex>, Set<DirectedHypergraph<T>.Vertex>) - Constructor for class mx.unam.iimas.griffin.graph.DirectedHypergraph.DirectedHyperEdge
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Creates the hyperedge
- DirectedHypergraph<T> - Class in mx.unam.iimas.griffin.graph
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A directed hypergraph
- DirectedHypergraph(Set<DirectedHypergraph<T>.Vertex>, Set<DirectedHypergraph<T>.DirectedHyperEdge>) - Constructor for class mx.unam.iimas.griffin.graph.DirectedHypergraph
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Creates the graph
- DirectedHypergraph.DirectedHyperEdge - Class in mx.unam.iimas.griffin.graph
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A directed hyperedge
- DirectedHypergraph.Vertex - Class in mx.unam.iimas.griffin.graph
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A vertex of the hypergraph
- doneWithFactory() - Method in class mx.unam.iimas.griffin.bdd.BDDModule
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Signals factory destruction
- DubrovaAttractors - Class in mx.unam.iimas.griffin.grn.util
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Obtains the set of all attractors for the given Boolean Network
- DubrovaAttractors(BooleanGeneRegulatoryNetwork) - Constructor for class mx.unam.iimas.griffin.grn.util.DubrovaAttractors
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Creates the class specifying the Boolean network
- DubrovaAttractors(BooleanGeneRegulatoryNetwork, ModelIterator) - Constructor for class mx.unam.iimas.griffin.grn.util.DubrovaAttractors
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Creates the class specifying the Boolean network and the model iterator