- ClauseBlocker - Interface in mx.unam.iimas.griffin.sat
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A clause blocker prevents an incremental SAT solver from finding models
having certain properties
- close() - Method in class mx.unam.iimas.griffin.grn.explorer.io.HierarchicalModelWriter
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Closes all file writers
- closeReader(BufferedReader) - Static method in class mx.unam.iimas.griffin.grn.explorer.io.FileUtil
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Closes the file reader
- closeWriter(BufferedWriter) - Static method in class mx.unam.iimas.griffin.grn.explorer.io.FileUtil
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Closes the file writer
- CNFConverter - Interface in mx.unam.iimas.griffin.sat
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CNF converter
A standarised interface for converting a sentence to conjunctive normal form
(CNF)
- Combinations - Class in mx.unam.iimas.griffin.math
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Combinations of a set
Implementation of the algorithm:
Phillip J.
- Combinations(int, int) - Constructor for class mx.unam.iimas.griffin.math.Combinations
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Creates the combinations object
- compareTo(BooleanNetworkState) - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkState
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- compareTo(BooleanNetworkStateTrajectory) - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkStateTrajectory
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- compareTo(Gene) - Method in class mx.unam.iimas.griffin.grn.Gene
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- compareTo(GeneInteraction) - Method in class mx.unam.iimas.griffin.grn.GeneInteraction
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- compareTo(GeneRegulation) - Method in class mx.unam.iimas.griffin.grn.GeneRegulation
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- compareTo(GeneState) - Method in class mx.unam.iimas.griffin.grn.GeneState
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- compareTo(InputOutputStatePair) - Method in class mx.unam.iimas.griffin.grn.InputOutputStatePair
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- compareTo(MutantExperiment) - Method in class mx.unam.iimas.griffin.grn.MutantExperiment
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- compareTo(StateTransitionRule) - Method in class mx.unam.iimas.griffin.grn.StateTransitionRule
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- compareTo(SynchronousAttractorBasin) - Method in class mx.unam.iimas.griffin.grn.SynchronousAttractorBasin
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- compareTo(Literal) - Method in class mx.unam.iimas.griffin.logic.Literal
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- compareTo(Variable) - Method in class mx.unam.iimas.griffin.logic.Variable
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- compatible(Set<BooleanNetworkState>, BooleanNetworkState) - Static method in class mx.unam.iimas.griffin.grn.explorer.attractor.AttractorUtil
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Checks whether the provided state is compatible with the set of states
- computeFunctionalDistance(BooleanGeneRegulatoryNetwork, BooleanGeneRegulatoryNetwork) - Method in class mx.unam.iimas.griffin.grn.util.Metrics
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Computes the functional distance
- computeTopologicalDistance(Set<GeneRegulation>, Set<GeneRegulation>) - Method in class mx.unam.iimas.griffin.grn.util.Metrics
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Computes the topological distance
- computeTopologicalDistance(String[], String[]) - Method in class mx.unam.iimas.griffin.grn.util.Metrics
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Computes topological distances using the basic string representation of
regulations
examples of string representations of regulations are: A+B, GEN1-GEN3,
SHR+JKD meaning positive regulation from A to B, negative regulation from
GEN1 to GEN3 and positive regulation from SHR to JKD respectively.
- consolidateAnd(Formula, Formula) - Static method in class mx.unam.iimas.griffin.logic.util.FormulaUtil
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Updates the formula to include the new sub-formula by using conjunction
- consolidateOr(Formula, Formula) - Static method in class mx.unam.iimas.griffin.logic.util.FormulaUtil
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Updates the formula to include the new sub-formula by using disjunction
- count(BDD) - Method in class mx.unam.iimas.griffin.grn.util.SynchronousSteadyStateAnalyzer
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Obtains the number of elements in the set
- countAssignedVariables() - Method in class mx.unam.iimas.griffin.bdd.QueryableAssignment
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Obtains the number of assigned variables
- createReader(String) - Static method in class mx.unam.iimas.griffin.grn.explorer.io.FileUtil
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Creates the file reader
- createWriter(String) - Static method in class mx.unam.iimas.griffin.grn.explorer.io.FileUtil
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Creates the file writer
- CrossDistance - Class in mx.unam.iimas.griffin.grn.explorer
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Cross distance calculator
- CrossDistance() - Constructor for class mx.unam.iimas.griffin.grn.explorer.CrossDistance
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