- imageOfSet(BDD) - Method in class mx.unam.iimas.griffin.grn.util.SteadyStateAnalyzer
-
finds the image of a given set of states represented with a Binary
Decision Diagram
- Implication - Class in mx.unam.iimas.griffin.logic
-
An implication tree formula
- Implication(Formula, Formula) - Constructor for class mx.unam.iimas.griffin.logic.Implication
-
Creates the implication formula tree
- IncrementalDistanceIterator - Class in mx.unam.iimas.griffin.grn.explorer.topology
-
Incremental distance iterator
Explores all possible topologies consistent with the hypotheses by
incremental topological distance.
- IncrementalDistanceIterator(Set<GeneInteraction>, int) - Constructor for class mx.unam.iimas.griffin.grn.explorer.topology.IncrementalDistanceIterator
-
Creates the iterator
- IncrementalDistanceIterator(InteractionClassifier, int) - Constructor for class mx.unam.iimas.griffin.grn.explorer.topology.IncrementalDistanceIterator
-
Creates the iterator
- info(String) - Method in class mx.unam.iimas.griffin.grn.explorer.io.HierarchicalModelWriter
-
Logs information for the current topology
- initialize() - Method in class mx.unam.iimas.griffin.grn.explorer.io.HierarchicalModelWriter
-
Initializes the root directory
- INPUT - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Name for capture group representing an input state
- INPUT_OUTPUT_PAIR - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Regular expression matching a boolean state input-output pair
- InputOutputEncoder - Class in mx.unam.iimas.griffin.grn.code
-
Encoder for input-output state pairs
- InputOutputEncoder() - Constructor for class mx.unam.iimas.griffin.grn.code.InputOutputEncoder
-
- InputOutputPairsValue - Class in mx.unam.iimas.griffin.grn.explorer.io
-
Value for input-output state pairs
- InputOutputPairsValue(String, Map<Integer, Gene>) - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.InputOutputPairsValue
-
Creates the Value for the given string
- InputOutputStatePair - Class in mx.unam.iimas.griffin.grn
-
Input-output state pair
- InputOutputStatePair(BooleanNetworkState, BooleanNetworkState) - Constructor for class mx.unam.iimas.griffin.grn.InputOutputStatePair
-
Creates the input-output pair
- InputVariant - Enum in mx.unam.iimas.griffin.grn.models.epistasis
-
Variant for input nodes
- INTERACTION_ACRONYM - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Name for capture group of interaction acronyms
- INTERACTION_LIST - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Name for capture group of the interactions list
- INTERACTION_PAIR - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Regular expression for individual interactions
- INTERACTION_TYPES - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
-
Regular expression for generalized interactions
- InteractionClassifier - Class in mx.unam.iimas.griffin.grn.explorer.topology
-
Classifies lists of gene interactions in several groups
core: interactions that are totally defined (known) and therefore don't give
place to variations variable: interactions that are not completely specified,
that is can take one of several options variable mandatory: variable
interactions that cannot instantiate to empty regulations
- InteractionClassifier(Set<GeneInteraction>) - Constructor for class mx.unam.iimas.griffin.grn.explorer.topology.InteractionClassifier
-
Creates the classifier for the set of interactions
- Interpretation - Class in mx.unam.iimas.griffin.logic
-
Propositional interpretation is a particular assignment for the propositional
variables
- Interpretation() - Constructor for class mx.unam.iimas.griffin.logic.Interpretation
-
- InterpretationUtil - Class in mx.unam.iimas.griffin.logic.util
-
Utility class for interpretations
- InterpretationUtil() - Constructor for class mx.unam.iimas.griffin.logic.util.InterpretationUtil
-
- Interval<T> - Class in mx.unam.iimas.griffin.math
-
An interval of numbers
- Interval(T, T) - Constructor for class mx.unam.iimas.griffin.math.Interval
-
Creates the interval
- isAdditionalCycles() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
If additional cycles (attractors with length greater than one) are
allowed
- isAdditionalSteadyStates() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
If additional steady states are allowed
- isAmbiguityNotAllowed() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
If ambiguity (positive and negative regulations by the same gene) are
allowed
- isAssigned(Variable) - Method in class mx.unam.iimas.griffin.bdd.QueryableAssignment
-
true if the variable has been assigned a particular value
- isBlockSteadyAPosteriori() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
if blocking of steady states is performed a posteriori
- isCyclic() - Method in class mx.unam.iimas.griffin.grn.BooleanNetworkStateTrajectory
-
Whether the trajectory is cyclic
- isDivideQueryByTopology() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
if the query will be split in many small queries
- isEdgeVariable(Variable) - Method in class mx.unam.iimas.griffin.grn.code.analysis.KlarnerEncoder
-
Determines if a varname is an edge variable
- isExactRegulations() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
If hypothesis are considered in the search
- isHypothetical() - Method in enum mx.unam.iimas.griffin.grn.GeneInteractionType
-
Whether the interaction is hypothetical or not
- isIterationMode() - Method in class mx.unam.iimas.griffin.grn.explorer.io.OutputFileParser
-
Determines the iteration mode
- isLimitTopologyRange() - Method in class mx.unam.iimas.griffin.grn.explorer.GeneRegulationSpecification
-
Whether there is a limited range of exploration for the topologies
- isMutantGene(Gene) - Method in class mx.unam.iimas.griffin.grn.MutantExperiment
-
Determines whether the gene has been mutated or not
- isPositive() - Method in class mx.unam.iimas.griffin.logic.Literal
-
Whether the literal is positive
- isRegulationVariable(Literal) - Static method in class mx.unam.iimas.griffin.grn.code.EncoderUtil
-
Verifies that the literal contains a regulation variable (It is
considered a regulation variable if its name contains the reserved
prefix)
- isTrueValueTable() - Method in class mx.unam.iimas.griffin.logic.implicants.MintermTable
-
True when the table represents true value function false otherwise
- isVertexVariable(Variable) - Method in class mx.unam.iimas.griffin.grn.code.analysis.KlarnerEncoder
-
Determines if a varname is a vertex variable