- RadialTopologyIterator - Class in mx.unam.iimas.griffin.grn.explorer.topology
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Incremental distance exploration strategy
- RadialTopologyIterator(Set<GeneInteraction>, int) - Constructor for class mx.unam.iimas.griffin.grn.explorer.topology.RadialTopologyIterator
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Creates the iterator
- random(Set<Variable>) - Static method in class mx.unam.iimas.griffin.logic.Interpretation
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Creates a random interpretation given the variables
- randomState() - Method in class mx.unam.iimas.griffin.grn.util.SteadyStateAnalyzer
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Generates a random state
- read() - Method in class mx.unam.iimas.griffin.grn.explorer.io.SpecificationFileReader
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Obtains the specification from the file
- readFile() - Method in class mx.unam.iimas.griffin.grn.explorer.util.FileReader
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Reads the contents of the file
- readNetworks(String) - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser
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Recovers networks from files
- readNextNetwork() - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser
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Obtains the following network
It is required to set have set the iterationMode to true
- readPrefixes(String) - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser
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Read prefixes file and prepare variables
- REGEXP_REGULATION_VARIABLE - Static variable in class mx.unam.iimas.griffin.grn.code.EncoderUtil
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Regular expression for parsing elements of regulations
- REGULATED - Static variable in class mx.unam.iimas.griffin.grn.code.EncoderUtil
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Regulated gene capture group name
- RegulationFormulaPair - Class in mx.unam.iimas.griffin.grn.code
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A pair of formulas for regulation
- RegulationFormulaPair(Dependency<Gene>, Set<Gene>) - Constructor for class mx.unam.iimas.griffin.grn.code.RegulationFormulaPair
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Creates a regulation formula pair
Positive and negative regulations for given genes
- REGULATOR - Static variable in class mx.unam.iimas.griffin.grn.code.EncoderUtil
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Regulator gene capture group name
- remove() - Method in class mx.unam.iimas.griffin.grn.explorer.topology.StructureIterator
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- remove() - Method in class mx.unam.iimas.griffin.sat.ModelIterator
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- removeComments(String) - Static method in class mx.unam.iimas.griffin.grn.explorer.io.GeneRegulationFileParser
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Removes user comment lines
- resetSolver(Formula) - Method in class mx.unam.iimas.griffin.sat.ModelIterator
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Resets the solver with a new formula This method reuses the thread
- rewrite(BDD, Map<Integer, Integer>) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
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Rewrites the variables of the provided BDD using the rewriting map
MODIFYING the original BDD
- rewrite(String, Map<Integer, Integer>) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
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Rewrites the BDD with the name given using the rewriting map
- rewriteVars(BDD, Map<Variable, Variable>) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
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rewrites the provided BDD variables according to the given map
- rewriteVars(String, Map<Variable, Variable>) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
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Rewrites the BDD with the name given using the rewriting map
- RIGHT - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
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Name for capture group representing right side of assignment
- RootStemCellNiche - Class in mx.unam.iimas.griffin.grn.models
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- RootStemCellNiche() - Constructor for class mx.unam.iimas.griffin.grn.models.RootStemCellNiche
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Construye la red
- RootStemCellNicheRevised - Class in mx.unam.iimas.griffin.grn.models
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- RootStemCellNicheRevised() - Constructor for class mx.unam.iimas.griffin.grn.models.RootStemCellNicheRevised
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Construye la red
- RULE - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
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Name for capture group representing a state transition rule