- RandomArrayList<E> - Class in org.gcn.plinguacore.util
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- RandomArrayList() - Constructor for class org.gcn.plinguacore.util.RandomArrayList
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- RandomArrayList(Collection<? extends E>) - Constructor for class org.gcn.plinguacore.util.RandomArrayList
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- RandomArrayList(int) - Constructor for class org.gcn.plinguacore.util.RandomArrayList
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- RandomNumbersGenerator - Class in org.gcn.plinguacore.util
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- Ratio - Class in org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule
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This class tests if the rule holds a float constant which is between 0 and 1
(the constant represents a probability)
- Ratio() - Constructor for class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.Ratio
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Creates a new Ratio instance, which checks only the restrictions defined on itself.
- Ratio(CheckRule) - Constructor for class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.Ratio
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Creates a new Ratio instance, which wraps cr as stated
by Decorator pattern.
- read(byte[], int, int) - Method in class org.gcn.plinguacore.parser.input.byteCounter.InputStreamWrapper
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- read(byte[]) - Method in class org.gcn.plinguacore.parser.input.byteCounter.InputStreamWrapper
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- read() - Method in class org.gcn.plinguacore.parser.input.byteCounter.InputStreamWrapper
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- read(char[], int, int) - Method in class org.gcn.plinguacore.parser.input.byteCounter.StringReaderWrapper
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- read() - Method in class org.gcn.plinguacore.parser.input.byteCounter.StringReaderWrapper
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- readChar() - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream
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- ReInit(Reader, int, int, int) - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream
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- ReInit(Reader, int, int) - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream
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- ReInit(Reader) - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream
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- ReInit(InputStream, String, int, int, int) - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream
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- ReInit(InputStream, int, int, int) - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream
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- ReInit(InputStream, String) - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream
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- ReInit(InputStream) - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream
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- ReInit(InputStream, String, int, int) - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream
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- ReInit(InputStream, int, int) - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream
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- remove(Object) - Method in class org.gcn.plinguacore.util.ExtendedLinkedHashSet
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- remove(Object, long) - Method in class org.gcn.plinguacore.util.HashInfiniteMultiSet
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- remove(Object) - Method in class org.gcn.plinguacore.util.HashInfiniteMultiSet
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- remove(Object, long) - Method in class org.gcn.plinguacore.util.HashMultiSet
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- remove(Object) - Method in class org.gcn.plinguacore.util.HashMultiSet
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- remove(Object, long) - Method in class org.gcn.plinguacore.util.InmutableMultiSet
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- remove(Object) - Method in class org.gcn.plinguacore.util.InmutableMultiSet
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- remove(Object, long) - Method in interface org.gcn.plinguacore.util.MultiSet
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Remove several objects of the multiset
- remove(Object) - Method in class org.gcn.plinguacore.util.psystem.rule.RulesSet
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- remove() - Method in class org.gcn.plinguacore.util.ShuffleIterator
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- remove() - Method in class org.gcn.plinguacore.util.UnionIterator
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- remove(Object) - Method in class org.gcn.plinguacore.util.UnionSet
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- removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.ExtendedLinkedHashSet
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- removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.HashInfiniteMultiSet
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- removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.HashMultiSet
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- removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.InmutableMultiSet
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- removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.psystem.rule.RulesSet
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- removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.UnionSet
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- removeLeftHandRuleObjects(CellLikeConfiguration, String) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.DynamicMatrix
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- removeLeftHandRuleObjects(CellLikeSkinMembrane, Map<String, Integer>, String, long) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentRulesBlock
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- removeLeftHandRuleObjects(CellLikeSkinMembrane, Map<String, Integer>, String, long) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixColumn
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- removeLeftHandRuleObjects(CellLikeSkinMembrane, Map<String, Integer>, String, long) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonRulesBlock
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- removeSpikes(long) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane
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- renewLabel(String) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane
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- replace(String, String) - Method in class org.gcn.plinguacore.util.GeneString
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Replaces the string s according to this gene string with the
string replacement.
- reset() - Method in class org.gcn.plinguacore.parser.input.byteCounter.InputStreamWrapper
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- reset() - Method in class org.gcn.plinguacore.simulator.AbstractSelectionExecutionSimulator
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- reset() - Method in class org.gcn.plinguacore.simulator.AbstractSimulator
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- reset() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.AbstractDnd2Sim
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- reset() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.AbstractDndProbabilisticSimulator
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- reset() - Method in class org.gcn.plinguacore.simulator.CopyOfAbstractSimulator
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Resets the simulator to the initial configuration
- reset() - Method in class org.gcn.plinguacore.simulator.DecoratorSimulator
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- reset() - Method in interface org.gcn.plinguacore.simulator.ISimulator
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Resets the simulator to the initial configuration
- reset() - Method in class org.gcn.plinguacore.simulator.StepBackSupportedSimulator
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- retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.ExtendedLinkedHashSet
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- retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.HashInfiniteMultiSet
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- retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.HashMultiSet
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- retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.InmutableMultiSet
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- retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.psystem.rule.RulesSet
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- retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.UnionSet
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- retainColumn(CellLikeSkinMembrane, Map<String, Integer>, String) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentRulesBlock
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- retainColumn(CellLikeSkinMembrane, Map<String, Integer>, String) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixColumn
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- retainColumn(CellLikeSkinMembrane, Map<String, Integer>, String) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonRulesBlock
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- retainRow(CellLikeSkinMembrane, Map<String, Integer>, String) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixRow
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- RightHandRule - Class in org.gcn.plinguacore.util.psystem.rule
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This class represents right hand rules
- RightHandRule(OuterRuleMembrane, MultiSet<String>) - Constructor for class org.gcn.plinguacore.util.psystem.rule.RightHandRule
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Creates a new
RightHandRule instance with the outer membrane and
the outer multiset passed as parameters.
- RightHandRule(OuterRuleMembrane, OuterRuleMembrane, MultiSet<String>) - Constructor for class org.gcn.plinguacore.util.psystem.rule.RightHandRule
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Creates a new
RightHandRule instance with the outer membrane, the
outer membrane resulting from division and the outer multiset passed as
parameters.
- RuleComparator - Class in org.gcn.plinguacore.util.psystem.rule
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- RuleComparator() - Constructor for class org.gcn.plinguacore.util.psystem.rule.RuleComparator
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- RulesSet - Class in org.gcn.plinguacore.util.psystem.rule
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A Set for rules
- RulesSet() - Constructor for class org.gcn.plinguacore.util.psystem.rule.RulesSet
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Constructs an empty RulesSet
- RulesSet(Collection<? extends IRule>) - Constructor for class org.gcn.plinguacore.util.psystem.rule.RulesSet
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Constructs a RulesSet with initial rules
- RulesSet(SortedSet<AlphabetObject>) - Constructor for class org.gcn.plinguacore.util.psystem.rule.RulesSet
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Constructs a RulesSet and update the alphabet passed as argument each time a new IRule is added to the set
- run() - Method in class org.gcn.plinguacore.simulator.AbstractSimulator
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Takes steps until reaching a halting configuration
- run() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.DndProbabilisticSelExecThread
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- run() - Method in class org.gcn.plinguacore.simulator.DecoratorSimulator
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- run() - Method in interface org.gcn.plinguacore.simulator.ISimulator
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Runs the simulator until reaching a halting configuration
- runSteps(int) - Method in class org.gcn.plinguacore.simulator.AbstractSimulator
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- runSteps(int) - Method in class org.gcn.plinguacore.simulator.DecoratorSimulator
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- runSteps(int) - Method in interface org.gcn.plinguacore.simulator.ISimulator
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Takes a specified number of steps
- runUntilTimeOut(long) - Method in class org.gcn.plinguacore.simulator.AbstractSimulator
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- runUntilTimeOut(long) - Method in class org.gcn.plinguacore.simulator.DecoratorSimulator
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- runUntilTimeOut(long) - Method in interface org.gcn.plinguacore.simulator.ISimulator
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Runs the simulator until the time out has been reached
- runUntilTimeOutorSteps(long, int) - Method in class org.gcn.plinguacore.simulator.AbstractSimulator
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- runUntilTimeOutorSteps(long, int) - Method in class org.gcn.plinguacore.simulator.DecoratorSimulator
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- runUntilTimeOutorSteps(long, int) - Method in interface org.gcn.plinguacore.simulator.ISimulator
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Runs the simulator until whether the time out or the steps have been
reached