- Parameters - Class in mx.unam.iimas.griffin.grn.explorer
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Search parameters
- Parameters() - Constructor for class mx.unam.iimas.griffin.grn.explorer.Parameters
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- parse(String) - Static method in class mx.unam.iimas.griffin.grn.explorer.io.BooleanNetworkTruthTableFileParser
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Parses the input obtaining a Boolean network
- parse(String) - Static method in class mx.unam.iimas.griffin.grn.explorer.io.GeneRegulationFileParser
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Obtains the gene regulation specification from the input
- parse() - Method in interface mx.unam.iimas.griffin.logic.parser.BooleanExpressionParser
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Obtains the tree formula representation of a Boolean expression
- parse(String) - Static method in class mx.unam.iimas.griffin.logic.parser.SimpleBooleanExpressionParser
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Parses the given expression
- parse() - Method in class mx.unam.iimas.griffin.logic.parser.SimpleBooleanExpressionParser
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- ParseException - Exception in mx.unam.iimas.griffin.logic.parser
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Error when parsing a Boolean expression
- ParseException() - Constructor for exception mx.unam.iimas.griffin.logic.parser.ParseException
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- ParseException(String, Throwable, boolean, boolean) - Constructor for exception mx.unam.iimas.griffin.logic.parser.ParseException
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Constructs a new runtime exception with the specified detail
message, cause, suppression enabled or disabled, and writable
stack trace enabled or disabled.
- ParseException(String, Throwable) - Constructor for exception mx.unam.iimas.griffin.logic.parser.ParseException
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Constructs a new runtime exception with the specified detail message and
cause.
- ParseException(String) - Constructor for exception mx.unam.iimas.griffin.logic.parser.ParseException
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Constructs a new runtime exception with the specified detail message.
- ParseException(Throwable) - Constructor for exception mx.unam.iimas.griffin.logic.parser.ParseException
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Constructs a new runtime exception with the specified cause and a
detail message of (cause==null ? null : cause.toString())
(which typically contains the class and detail message of
cause).
- parseGene(String) - Method in class mx.unam.iimas.griffin.grn.explorer.io.UpdateRulesValue
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Obtains the parsed gene
- parseNegatedStates(String, int, Map<Integer, Gene>) - Static method in class mx.unam.iimas.griffin.grn.explorer.io.ParserHelper
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Parses the states
The list only includes negated states
- ParserHelper - Class in mx.unam.iimas.griffin.grn.explorer.io
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Auxiliary methods for parsing
- ParserHelper() - Constructor for class mx.unam.iimas.griffin.grn.explorer.io.ParserHelper
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- parseState(String, Map<Integer, Gene>) - Static method in class mx.unam.iimas.griffin.grn.explorer.io.ParserHelper
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Parses the input as a state
- parseStates(String, int, Map<Integer, Gene>) - Static method in class mx.unam.iimas.griffin.grn.explorer.io.ParserHelper
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Parses the states
The list does not exclude negated states
- parseTable(String, List<Variable>) - Static method in class mx.unam.iimas.griffin.grn.util.TruthTableParser
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Parses a table of boolean values and returns the corresponding DNF
sentence
- parseValue() - Method in class mx.unam.iimas.griffin.grn.explorer.io.GeneListValue
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Parses the input
- parseVariables(String) - Static method in class mx.unam.iimas.griffin.grn.util.TruthTableParser
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Parses a set of variables
- parseVariables(String) - Static method in class mx.unam.iimas.griffin.logic.parser.SimpleBooleanExpressionParser
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Parses the set of variables contained within the given expression
- PartialBooleanNetworkState - Class in mx.unam.iimas.griffin.grn
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- PartialBooleanNetworkState(int) - Constructor for class mx.unam.iimas.griffin.grn.PartialBooleanNetworkState
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Creates the state
- PLACE_HOLDER - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
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Place holder for parameter substitution
- POSITIVE_REGULATION - Static variable in class mx.unam.iimas.griffin.grn.explorer.io.FileRegExp
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Regular expression matching a positive regulation
- preImageOfSet(BDD) - Method in class mx.unam.iimas.griffin.grn.util.SteadyStateAnalyzer
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finds the pre-image of a given set of states represented with a Binary
Decision Diagram
- prime(Variable) - Static method in class mx.unam.iimas.griffin.grn.util.TransitionRelation
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Obtains the variable representing the given variable for the following
time (prime variable)
- PrimeImplicant - Class in mx.unam.iimas.griffin.logic.implicants
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Prime implicant for a given function
- PrimeImplicant(List<Literal>, boolean) - Constructor for class mx.unam.iimas.griffin.logic.implicants.PrimeImplicant
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Creates the prime implicant
- PrimeImplicantGraph - Class in mx.unam.iimas.griffin.logic.implicants
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- PrimeImplicantGraph(Set<DirectedHypergraph<Literal>.Vertex>, Set<DirectedHypergraph<Literal>.DirectedHyperEdge>) - Constructor for class mx.unam.iimas.griffin.logic.implicants.PrimeImplicantGraph
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- PrimeImplicantGraph(BooleanGeneRegulatoryNetwork) - Constructor for class mx.unam.iimas.griffin.logic.implicants.PrimeImplicantGraph
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- PropositionalModel - Class in mx.unam.iimas.griffin.sat
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A list of literals used as a representation of a satisfying assignment for a
certain formula
- PropositionalModel(int[], CNFConverter) - Constructor for class mx.unam.iimas.griffin.sat.PropositionalModel
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Creates a model given an encoding