- main(String[]) - Static method in class mx.unam.iimas.griffin.grn.experiment.WeinsteinTopologyExplorationAmbiguityAllowed
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- main(String[]) - Static method in class mx.unam.iimas.griffin.grn.explorer.AttractorSetExplorer
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Plain main method, no command line arguments
- main(String[]) - Static method in class mx.unam.iimas.griffin.grn.explorer.Basins
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Computes the cross distance
- main(String[]) - Static method in class mx.unam.iimas.griffin.grn.explorer.CrossDistance
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Computes the cross distance
- main(String[]) - Static method in class mx.unam.iimas.griffin.grn.explorer.Griffin
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GRIFFIN Main
- main(String[]) - Static method in class mx.unam.iimas.griffin.grn.explorer.GriffinBackup
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GRIFFIN Main
- match(Integer, Integer) - Static method in class mx.unam.iimas.griffin.logic.implicants.MintermMatching
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Creates the matching if conditions are satisfied
- match(MintermMatching, MintermMatching) - Static method in class mx.unam.iimas.griffin.logic.implicants.MintermMatching
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Creates the matching if conditions are satisfied
- Metrics - Class in mx.unam.iimas.griffin.grn.util
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Network metrics
- Metrics(int) - Constructor for class mx.unam.iimas.griffin.grn.util.Metrics
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Creates and initializes the Metrics object
- Metrics() - Constructor for class mx.unam.iimas.griffin.grn.util.Metrics
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Creates and initializes the Metrics object
- MintermMatching - Class in mx.unam.iimas.griffin.logic.implicants
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A matching of minterms with one or more fictitious variables, that is,
variables that are not essential for the implicant
- MintermTable - Class in mx.unam.iimas.griffin.logic.implicants
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Minterm table
Classifies all minterms of a truth table according to the number of ones of
their binary representation and the truth value they evaluate to
- MintermTable(TruthTable, boolean) - Constructor for class mx.unam.iimas.griffin.logic.implicants.MintermTable
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Creates the minterm table
- MintermToImplicant(Integer, SortedSet<Variable>, boolean) - Static method in class mx.unam.iimas.griffin.logic.implicants.util.MintermUtil
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Obtains the prime implicant of a given minterm
- MintermUtil - Class in mx.unam.iimas.griffin.logic.implicants.util
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Utility methods for minterms
- MintermUtil() - Constructor for class mx.unam.iimas.griffin.logic.implicants.util.MintermUtil
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- ModelDecoder - Class in mx.unam.iimas.griffin.util
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Helper class for model decoding
- ModelDecoder() - Constructor for class mx.unam.iimas.griffin.util.ModelDecoder
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- ModelIterator - Class in mx.unam.iimas.griffin.sat
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Iterates over all models of a sentence
- ModelIterator(Formula, ClauseBlocker) - Constructor for class mx.unam.iimas.griffin.sat.ModelIterator
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Creates a model iterator
Specifies a class for custom blocking of clauses The incremental SAT
solver calls this class to prune search space according to its blocking
method and the models found by the solver
- ModelIterator(Formula, ClauseBlocker, boolean) - Constructor for class mx.unam.iimas.griffin.sat.ModelIterator
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Creates a model iterator
Specifies a class for custom blocking of clauses The incremental SAT
solver calls this class to prune search space according to its blocking
method and the models found by the solver
- ModelIterator(Formula) - Constructor for class mx.unam.iimas.griffin.sat.ModelIterator
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Creates a model iterator
- ModelIterator(Formula, boolean) - Constructor for class mx.unam.iimas.griffin.sat.ModelIterator
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Creates a model iterator
- ModelPrinter - Class in mx.unam.iimas.griffin.util
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Auxiliary class for converting models to Strings
- ModelPrinter() - Constructor for class mx.unam.iimas.griffin.util.ModelPrinter
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- modelToString(PropositionalModel, KlarnerEncoder) - Static method in class mx.unam.iimas.griffin.grn.code.analysis.KlarnerDecoder
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Converts models to their String representation considering only positive
literals which represent hyperedges of the prime implicant graph
- Motif - Class in mx.unam.iimas.griffin.grn.models.epistasis
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- Motif(InputVariant, TopologyVariant, MotifVariant) - Constructor for class mx.unam.iimas.griffin.grn.models.epistasis.Motif
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Creates the motif
- MotifVariant - Enum in mx.unam.iimas.griffin.grn.models.epistasis
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Motif variants
- MutantExperiment - Class in mx.unam.iimas.griffin.grn
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Experimental evidence for mutating a gene
- MutantExperiment(Set<GeneState>, Set<BooleanNetworkState>) - Constructor for class mx.unam.iimas.griffin.grn.MutantExperiment
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Creates the mutant experiment
- MutantExperimentEncoder - Class in mx.unam.iimas.griffin.grn.code
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Encoder for mutant experiments
- MutantExperimentEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.MutantExperimentEncoder
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- MutantExperimentSetValue - Class in mx.unam.iimas.griffin.grn.explorer.io
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- MutantExperimentSetValue(String) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.MutantExperimentSetValue
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- MutantExperimentSetValue(String, Map<Integer, Gene>) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.MutantExperimentSetValue
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- mx.unam.iimas.griffin.graph - package mx.unam.iimas.griffin.graph
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Classes for Graph representations
- mx.unam.iimas.griffin.grn.code - package mx.unam.iimas.griffin.grn.code
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Classes for encoding and decoding queries
- mx.unam.iimas.griffin.grn.code.analysis - package mx.unam.iimas.griffin.grn.code.analysis
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Classes for analyzing network dynamics
- mx.unam.iimas.griffin.grn.experiment - package mx.unam.iimas.griffin.grn.experiment
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Examples of programmatic queries
- mx.unam.iimas.griffin.grn.explorer.attractor - package mx.unam.iimas.griffin.grn.explorer.attractor
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- mx.unam.iimas.griffin.grn.explorer.topology - package mx.unam.iimas.griffin.grn.explorer.topology
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Classes for topology (network structure) queries
- mx.unam.iimas.griffin.grn.models - package mx.unam.iimas.griffin.grn.models
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Some examples of programmatically specified models
- mx.unam.iimas.griffin.grn.models.epistasis - package mx.unam.iimas.griffin.grn.models.epistasis
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Classes epistasis experiments
- mx.unam.iimas.griffin.logic.implicants.util - package mx.unam.iimas.griffin.logic.implicants.util
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Util classes for prime implicants
- mx.unam.iimas.griffin.math - package mx.unam.iimas.griffin.math
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- mx.unam.iimas.griffin.util - package mx.unam.iimas.griffin.util
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Classes for interacting with satisfying assignments