- obtainAmbiguousRegulations(Set<GeneRegulation>) - Static method in class mx.unam.iimas.griffin.grn.util.TopologyUtil
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Obtain ambiguous regulations
- obtainLiteralsMap(BooleanNetworkState, Map<Gene, Set<Gene>>) - Static method in class mx.unam.iimas.griffin.grn.code.FixedPointAttractorEncoder
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Encodes the given state as a map from gene to the set of literals for
which the conjunction represents a fixed point attractor
- obtainSimplifiedNotFixedPoints(BooleanGeneRegulatoryNetwork) - Static method in class mx.unam.iimas.griffin.grn.util.AsynchronousTransitionRelation
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Obtains the formula representing the asynchronous transition relation for
the Boolean Network, in this formula fixed points are left out
- obtainSynchronousFormula(BooleanGeneRegulatoryNetwork) - Static method in class mx.unam.iimas.griffin.grn.util.SynchronousTransitionRelation
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Obtains the formula representing the synchronous transition relation for
the Boolean Network
- obtainTransitionFunction(PropositionalModel, Gene, Set<Gene>) - Static method in class mx.unam.iimas.griffin.grn.code.GeneRegulationDeterministicDecoder
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Obtains the transition rule for given gene
- obtainVariables(Formula) - Static method in class mx.unam.iimas.griffin.logic.util.FormulaEvaluator
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Obtains the variables in the given formula
- ONE - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
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One character
- Operator - Enum in mx.unam.iimas.griffin.logic
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Boolean operator
- Or - Class in mx.unam.iimas.griffin.logic
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Or tree formula
- Or(Formula, Formula) - Constructor for class mx.unam.iimas.griffin.logic.Or
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Creates the Or tree formula
- OUTPUT - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
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Name for capture group representing an output state
- OutputFileParser - Class in mx.unam.iimas.griffin.grn.explorer.io
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Parser for output files
- OutputFileParser() - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser
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Creates the parser
- OutputFileParser(String[]) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser
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creates the parser for the provided file