A B C D E F G H I J L M N O P Q R S T U V W X

R

RandomArrayList<E> - Class in org.gcn.plinguacore.util

RandomArrayList() - Constructor for class org.gcn.plinguacore.util.RandomArrayList

RandomArrayList(Collection<? extends E>) - Constructor for class org.gcn.plinguacore.util.RandomArrayList

RandomArrayList(int) - Constructor for class org.gcn.plinguacore.util.RandomArrayList

RandomNumbersGenerator - Class in org.gcn.plinguacore.util

Ratio - Class in org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule

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

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

Creates a new Ratio instance, which wraps cr as stated by Decorator pattern.

RBRACE - Static variable in interface org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserConstants

read(byte[], int, int) - Method in class org.gcn.plinguacore.parser.input.byteCounter.InputStreamWrapper

read(byte[]) - Method in class org.gcn.plinguacore.parser.input.byteCounter.InputStreamWrapper

read() - Method in class org.gcn.plinguacore.parser.input.byteCounter.InputStreamWrapper

read(char[], int, int) - Method in class org.gcn.plinguacore.parser.input.byteCounter.StringReaderWrapper

read() - Method in class org.gcn.plinguacore.parser.input.byteCounter.StringReaderWrapper

ReInit(SimpleCharStream) - Method in class org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserTokenManager

ReInit(SimpleCharStream, int) - Method in class org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserTokenManager

remove(Object, long) - Method in class org.gcn.plinguacore.util.HashInfiniteMultiSet

remove(Object) - Method in class org.gcn.plinguacore.util.HashInfiniteMultiSet

remove(Object, long) - Method in class org.gcn.plinguacore.util.HashMultiSet

remove(Object) - Method in class org.gcn.plinguacore.util.HashMultiSet

remove(Object, long) - Method in class org.gcn.plinguacore.util.InmutableMultiSet

remove(Object) - Method in class org.gcn.plinguacore.util.InmutableMultiSet

remove(Object, long) - Method in interface org.gcn.plinguacore.util.MultiSet

Remove several objects of the multiset

remove(Object) - Method in class org.gcn.plinguacore.util.psystem.rule.RulesSet

remove() - Method in class org.gcn.plinguacore.util.ShuffleIterator

remove() - Method in class org.gcn.plinguacore.util.UnionIterator

remove(Object) - Method in class org.gcn.plinguacore.util.UnionSet

removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.HashInfiniteMultiSet

removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.HashMultiSet

removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.InmutableMultiSet

removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.psystem.rule.RulesSet

removeAll(Collection<?>) - Method in class org.gcn.plinguacore.util.UnionSet

replace(String, String) - Method in class org.gcn.plinguacore.util.GeneString

Replaces the string s according to this gene string with the string replacement.

reset() - Method in class org.gcn.plinguacore.parser.input.byteCounter.InputStreamWrapper

reset() - Method in class org.gcn.plinguacore.simulator.AbstractSelectionExecutionSimulator

reset() - Method in class org.gcn.plinguacore.simulator.AbstractSimulator

Resets the simulator to the initial configuration

reset() - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.DeterministicWaitingTimesSimulator

Re-build the data structures used in this algorithm

reset() - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.EfficientStochasticSimulator

Re-build the data structures used in this algorithm

reset() - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator

Sets the time of the stochastic simulation to zero and initializes the list of reactions, that is, a_i is recalculated for every reaction in the system.

reset() - Method in class org.gcn.plinguacore.simulator.DecoratorSimulator

reset() - Method in interface org.gcn.plinguacore.simulator.ISimulator

Resets the simulator to the initial configuration

reset() - Method in class org.gcn.plinguacore.simulator.StepBackSupportedSimulator

retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.HashInfiniteMultiSet

retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.HashMultiSet

retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.InmutableMultiSet

retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.psystem.rule.RulesSet

retainAll(Collection<?>) - Method in class org.gcn.plinguacore.util.UnionSet

RightHandRule - Class in org.gcn.plinguacore.util.psystem.rule

This class represents right hand rules

RightHandRule(OuterRuleMembrane, MultiSet<String>) - Constructor for class org.gcn.plinguacore.util.psystem.rule.RightHandRule

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

Creates a new RightHandRule instance with the outer membrane, the outer membrane resulting from division and the outer multiset passed as parameters.

ROUND - Static variable in interface org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserConstants

RPAR - Static variable in interface org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserConstants

RSQUARE - Static variable in interface org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserConstants

RuleComparator - Class in org.gcn.plinguacore.util.psystem.rule

RuleComparator() - Constructor for class org.gcn.plinguacore.util.psystem.rule.RuleComparator

RulesSet - Class in org.gcn.plinguacore.util.psystem.rule

A Set for rules

RulesSet() - Constructor for class org.gcn.plinguacore.util.psystem.rule.RulesSet

Constructs an empty RulesSet

RulesSet(Collection<? extends IRule>) - Constructor for class org.gcn.plinguacore.util.psystem.rule.RulesSet

Constructs a RulesSet with initial rules

RulesSet(SortedSet<AlphabetObject>) - Constructor for class org.gcn.plinguacore.util.psystem.rule.RulesSet

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

Takes steps until reaching a halting configuration

run() - Method in class org.gcn.plinguacore.simulator.DecoratorSimulator

run() - Method in interface org.gcn.plinguacore.simulator.ISimulator

Runs the simulator until reaching a halting configuration

runSteps(int) - Method in class org.gcn.plinguacore.simulator.AbstractSimulator

runSteps(int) - Method in class org.gcn.plinguacore.simulator.DecoratorSimulator

runSteps(int) - Method in interface org.gcn.plinguacore.simulator.ISimulator

Takes a specified number of steps

runUntilTimeOut(long) - Method in class org.gcn.plinguacore.simulator.AbstractSimulator

runUntilTimeOut(long) - Method in class org.gcn.plinguacore.simulator.DecoratorSimulator

runUntilTimeOut(long) - Method in interface org.gcn.plinguacore.simulator.ISimulator

Runs the simulator until the time out has been reached

runUntilTimeOutorSteps(long, int) - Method in class org.gcn.plinguacore.simulator.AbstractSimulator

runUntilTimeOutorSteps(long, int) - Method in class org.gcn.plinguacore.simulator.DecoratorSimulator

runUntilTimeOutorSteps(long, int) - Method in interface org.gcn.plinguacore.simulator.ISimulator

Runs the simulator until whether the time out or the steps have been reached