- SEPARATOR - Static variable in class mx.unam.iimas.griffin.grn.code.EncoderUtil
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Name-index separator for encoding variables
- SequentialTopologyIterator - Class in mx.unam.iimas.griffin.grn.explorer.topology
-
This class allows the iteration over all possible topologies given a set of
gene interactions
- SequentialTopologyIterator(Set<GeneInteraction>) - Constructor for class mx.unam.iimas.griffin.grn.explorer.topology.SequentialTopologyIterator
-
Creates the enumerator
- SequentialTopologyIterator(Set<GeneInteraction>, TopologyIteratorFilter) - Constructor for class mx.unam.iimas.griffin.grn.explorer.topology.SequentialTopologyIterator
-
Creates the iterator that will apply the filter to the provided
regulations
- set(Formula, String) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
-
Transforms the formula to BDD representation and give it the provided
name
- set(Variable) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
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Sets the provided variable in the module
- set(BDD, String) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
-
Creates or updates the BDD under the given name
- set(BDD) - Method in class mx.unam.iimas.griffin.bdd.BDDModule
-
Adds the provided BDD to the module the name of the bdd is the same as
that of its identifier the identifier is automatically generated
- setAdditionalCycles(boolean) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
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Sets the flag for additional cycles
- setAdditionalSteadyStates(boolean) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the flag for considering additional steady states
- setAmbiguityNotAllowed(boolean) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the flag for not allowing ambiguity
- setAttractors(Set<BooleanNetworkStateTrajectory>) - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetworkInfo
-
Sets the set of attractos for the Boolean network
- setBlockSteadyAPosteriori(boolean) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
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Sets the flag for blocking steady states a posteriori
- setCycles(Set<BooleanNetworkStateTrajectory>) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the cyclic attractors
- setDivideQueryByTopology(boolean) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
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- setExactRegulations(boolean) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
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Sets the flag for considering hypothesis
- setGeneInteractions(Set<GeneInteraction>) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the gene intaractions
- setGeneOrder(GeneOrder) - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetworkInfo
-
Sets the user defined ordering of the genes
- setGeneOrdering(GeneOrder) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the user defined ordering of the genes
- setGeneState(Gene, Boolean) - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkState
-
Establishes the value of the given gene
- setInputOutputPairs(Set<InputOutputStatePair>) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the input output pairs
- setIterationMode(boolean) - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser
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Sets the iteration mode
Activating iteration mode can only be established once
In iteration mode readPrefixes should be called after this method
- setLeft(String) - Method in class mx.unam.iimas.griffin.grn.explorer.io.AssignmentStatement
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Sets the left side of the assignment
- setLimitToNumberOfNetworks(int) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets a limit to the number of networks to explore -1 means no limit
- setNetwork(BooleanGeneRegulatoryNetwork) - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetworkInfo
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Sets the Boolean network
- setOutputFile(String) - Method in class mx.unam.iimas.griffin.grn.explorer.Griffin
-
sets the name of the output file
- setProhibitedStableStates(Set<BooleanNetworkState>) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the list of prohibited stable states
- setQueryFile(String) - Method in class mx.unam.iimas.griffin.grn.explorer.Griffin
-
sets the name of the query file
- setRight(String) - Method in class mx.unam.iimas.griffin.grn.explorer.io.AssignmentStatement
-
Sets the right side of the assignment
- setSpecification(GeneRegulationSpecification) - Method in class mx.unam.iimas.griffin.grn.code.GeneRegulationDeterministicEncoder
-
- setSpecification(GeneRegulationSpecification) - Method in interface mx.unam.iimas.griffin.grn.code.GeneRegulationEncoder
-
Sets the regulation specification for the encoding
- setSteadyStates(Set<BooleanNetworkState>) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the set of all steady states (wildtype fixed point attractors)
- setSubspaces(Set<BooleanNetworkState>) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the subspaces
- setTopologicalDistanceRadius(int) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the topological distance exploration radius for the radial iterator
- setTopology(Set<GeneRegulation>) - Method in class mx.unam.iimas.griffin.grn.BooleanGeneRegulatoryNetworkInfo
-
Sets the topology of the network
- setTopologyIteratorType(TopologyIteratorType) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the type of the topology iterator
- setTopologyRange(Interval<Integer>) - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Sets the range of topologies to explore
- setupTopology(Set<GeneRegulation>, int, int) - Method in class mx.unam.iimas.griffin.grn.explorer.io.HierarchicalModelWriter
-
Prepares the files required to log information to topology
- SIGN - Static variable in class mx.unam.iimas.griffin.grn.code.EncoderUtil
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Gene regulation sign capture group name
- simple() - Method in class mx.unam.iimas.griffin.logic.And
-
Simplifies against Boolean constants
- simple() - Method in class mx.unam.iimas.griffin.logic.Equality
-
Simplifies against Boolean constants
- simple() - Method in class mx.unam.iimas.griffin.logic.Not
-
Simplifies against Boolean constants
- simple() - Method in class mx.unam.iimas.griffin.logic.Or
-
Simplifies against Boolean constants
- SimpleBooleanExpressionParser - Class in mx.unam.iimas.griffin.logic.parser
-
Simple expression parser for Boolean expressions
- SimpleBooleanExpressionParser(String) - Constructor for class mx.unam.iimas.griffin.logic.parser.SimpleBooleanExpressionParser
-
Creates the parser for the given expression
- SINGLE_LINE_COMMENT - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Regular expression matching single line comments
- SOURCE - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Name for capture group representing source gene
- SpecificationFileReader - Class in mx.unam.iimas.griffin.grn.explorer.io
-
File reader for an specification file
- SpecificationFileReader(Path) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.SpecificationFileReader
-
Creates the reader
- SpecificationFileReader(String) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.SpecificationFileReader
-
Creates the reader for the specified file
- StableStatesFormulaPair - Class in mx.unam.iimas.griffin.grn.code
-
A pair of tree formula representations for stable and not stable states
- StableStatesFormulaPair(GeneRegulationSpecification, GeneRegulationDeterministicEncoder.HypotheticalRegulationPolicy, GeneRegulationDeterministicEncoder.StableStatesPolicy) - Constructor for class mx.unam.iimas.griffin.grn.code.StableStatesFormulaPair
-
Creates the encoding for stable states and not stable states
- stableStatesPolicy - Variable in class mx.unam.iimas.griffin.grn.code.GeneRegulationDeterministicEncoder
-
- StateTrajectoryEncoder - Class in mx.unam.iimas.griffin.grn.code
-
Encodes state space trajectories into Boolean formulas
- StateTrajectoryEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.StateTrajectoryEncoder
-
- StateTransitionRule - Class in mx.unam.iimas.griffin.grn
-
The transition function for a gene
- StateTransitionRule(Gene, Formula) - Constructor for class mx.unam.iimas.griffin.grn.StateTransitionRule
-
Creates the state transition rule for a given gene
- StateTransitionRuleEncoder - Class in mx.unam.iimas.griffin.grn.code
-
Encoder for state transition rules
- StateTransitionRuleEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.StateTransitionRuleEncoder
-
- StateUtil - Class in mx.unam.iimas.griffin.util
-
Util methods for network states
- StateUtil() - Constructor for class mx.unam.iimas.griffin.util.StateUtil
-
- SteadyStateAnalyzer - Class in mx.unam.iimas.griffin.grn.util
-
Analyzes steady state behavior of boolean networks
- SteadyStateAnalyzer(BooleanGeneRegulatoryNetwork) - Constructor for class mx.unam.iimas.griffin.grn.util.SteadyStateAnalyzer
-
Creates the analyzer for the given network
- SteadyStateAnalyzer(BooleanGeneRegulatoryNetwork, BDDModule) - Constructor for class mx.unam.iimas.griffin.grn.util.SteadyStateAnalyzer
-
- StructureBlocker - Class in mx.unam.iimas.griffin.grn.explorer.topology
-
Blocks topologies for an incremental SAT query
- StructureIterator - Class in mx.unam.iimas.griffin.grn.explorer.topology
-
Allows to iterate over structure
- StructureIterator(GeneRegulationSpecification, GeneRegulationDeterministicEncoder.StableStatesPolicy, boolean) - Constructor for class mx.unam.iimas.griffin.grn.explorer.topology.StructureIterator
-
Creates an iterator over the satisfying network structures
- StructureIterator(Formula) - Constructor for class mx.unam.iimas.griffin.grn.explorer.topology.StructureIterator
-
Creates an interator over the satisfying network structures for the given
formula.
- SubspaceEncoder - Class in mx.unam.iimas.griffin.grn.code
-
Encoder for subspaces
- SubspaceEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.SubspaceEncoder
-
- substitute(Variable, Formula) - Method in class mx.unam.iimas.griffin.logic.And
-
- substitute(Variable, Formula) - Method in class mx.unam.iimas.griffin.logic.BooleanConstant
-
- substitute(Variable, Formula) - Method in class mx.unam.iimas.griffin.logic.Equality
-
- substitute(Variable, Formula) - Method in interface mx.unam.iimas.griffin.logic.Formula
-
Substitutes the variable for the given formula
- substitute(Variable, Formula) - Method in class mx.unam.iimas.griffin.logic.Implication
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- substitute(Variable, Formula) - Method in class mx.unam.iimas.griffin.logic.Not
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- substitute(Variable, Formula) - Method in class mx.unam.iimas.griffin.logic.Or
-
- substitute(Variable, Formula) - Method in class mx.unam.iimas.griffin.logic.Variable
-
- SynchronousAttractorBasin - Class in mx.unam.iimas.griffin.grn
-
Basin of attraction for an attractor
The basin includes all states that converge to the attractor including the
attractor itself
- SynchronousAttractorBasin(BooleanNetworkStateTrajectory, BDD, BDD) - Constructor for class mx.unam.iimas.griffin.grn.SynchronousAttractorBasin
-
Creates the Basin of attraction
- SynchronousSteadyStateAnalyzer - Class in mx.unam.iimas.griffin.grn.util
-
Analyzes steady state behavior of boolean networks
- SynchronousSteadyStateAnalyzer(BooleanGeneRegulatoryNetwork) - Constructor for class mx.unam.iimas.griffin.grn.util.SynchronousSteadyStateAnalyzer
-
Creates the analyzer for the given network
- SynchronousSteadyStateAnalyzer(BooleanGeneRegulatoryNetwork, BDDModule) - Constructor for class mx.unam.iimas.griffin.grn.util.SynchronousSteadyStateAnalyzer
-
- SynchronousTransitionRelation - Class in mx.unam.iimas.griffin.grn.util
-
Synchronous transition relation for a Boolean Network
- SynchronousTransitionRelation() - Constructor for class mx.unam.iimas.griffin.grn.util.SynchronousTransitionRelation
-