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

S

saveElement() - Method in class org.gcn.plinguacore.simulator.ElementFileStream

Saves the element

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

setAbstractPsystemFactory(IPsystemFactory) - Method in class org.gcn.plinguacore.util.psystem.Psystem

Sets an specific instance of PsystemFactotyInterface as the current factory to be used

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

setAllObjectsWithInfiniteMultiplicity() - Method in interface org.gcn.plinguacore.util.InfiniteMultiSet

setCharge(byte) - Method in class org.gcn.plinguacore.util.psystem.membrane.ChangeableMembrane

Sets the membrane charge

setCheckRule(CheckRule) - Method in class org.gcn.plinguacore.util.psystem.rule.RulesSet

Set the CheckRule object for this RulesSet

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

Sets the current configuration of the simulator

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

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

Sets the current configuration of the simulator

setDebugStream(PrintStream) - Method in class org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserTokenManager

setElement(ElementType) - Method in class org.gcn.plinguacore.simulator.ElementFileStream

Sets the element to be saved

setErrorChannel(PrintStream) - Method in class org.gcn.plinguacore.parser.input.InputParser

Sets the PrintStream instance to write errors

setFile(String) - Method in class org.gcn.plinguacore.simulator.ElementFileStream

Sets the file where the current element will be saved on

setGlobalIndex(int) - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator.Reaction

setI(int) - Method in class org.gcn.plinguacore.util.IndexedPriorityQueue.Node

setIndex(int) - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator.Reaction

setInfoChannel(PrintStream) - Method in class org.gcn.plinguacore.parser.input.InputParser

Sets the PrintStream to write information

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

Sets the info channel

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

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

Sets the simulator info channel

setLeftChild(IndexedPriorityQueue<E>.Node<T>) - Method in class org.gcn.plinguacore.util.IndexedPriorityQueue.Node

setMembraneStructure(MembraneStructure) - Method in class org.gcn.plinguacore.util.psystem.cellLike.CellLikePsystem

setMembraneStructure(MembraneStructure) - Method in class org.gcn.plinguacore.util.psystem.Psystem

setMembraneStructure(MembraneStructure) - Method in class org.gcn.plinguacore.util.psystem.tissueLike.TissueLikePsystem

setMsgChannel(PrintStream) - Method in class org.gcn.plinguacore.parser.input.InputParser

Sets the PrintStream instance to write messages

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

Sets the number of output time steps Default is 50

setParent(IndexedPriorityQueue<E>.Node<T>) - Method in class org.gcn.plinguacore.util.IndexedPriorityQueue.Node

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

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

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

Sets the simulator P-system

setRightChild(IndexedPriorityQueue<E>.Node<T>) - Method in class org.gcn.plinguacore.util.IndexedPriorityQueue.Node

setT_1(double) - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator.Reaction

setTau(double) - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator.Reaction

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

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

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

Sets if the elapsed time is being measured or not

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

Sets the timeOut for the Gillespie simulation The default timeOut is 50

setValue(T) - Method in class org.gcn.plinguacore.util.IndexedPriorityQueue.Node

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

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

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

Sets the verbosity level which the instances take into account when reporting messages.

setVerbosityLevel(int) - Method in class org.gcn.plinguacore.parser.input.InputParser

Sets the verbosity level (usually between 0-5)

setWarningChannel(PrintStream) - Method in class org.gcn.plinguacore.parser.input.InputParser

Sets the PrintStream instance to write warnings

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

ShuffleIterator(List<E>) - Constructor for class org.gcn.plinguacore.util.ShuffleIterator

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

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

size() - Method in class org.gcn.plinguacore.util.IndexedPriorityQueue

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

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

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

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

sortByPriority(List<IRule>) - Static method in class org.gcn.plinguacore.util.psystem.rule.RulesSet

specificParse(InputStream, String[]) - Method in class org.gcn.plinguacore.parser.input.plingua.PlinguaInputParser

specificParse(StringReader, String[]) - Method in class org.gcn.plinguacore.parser.input.plingua.PlinguaInputParser

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

Makes one step of simulation and generate a new configuration

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

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

Takes one step of simulation and generate a new configuration

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

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

Makes one step back.

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

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

Takes one step back

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

StepBackSupportedSimulator - Class in org.gcn.plinguacore.simulator

This class is intended to be extended by classes which provide functionality to take steps back, according to Decorator pattern

StepBackSupportedSimulator(ISimulator) - Constructor for class org.gcn.plinguacore.simulator.StepBackSupportedSimulator

Creates a new StepBackSupportedSimulator instance which will wrap sim

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

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

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

Returns a boolean representing if there are any step back which the simulator can go back to

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

StochasticCreateSimulator - Class in org.gcn.plinguacore.simulator.cellLike.stochastic

StochasticCreateSimulator(String) - Constructor for class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticCreateSimulator

StochasticPsystemFactory - Class in org.gcn.plinguacore.simulator.cellLike.stochastic

StochasticSimulator - Class in org.gcn.plinguacore.simulator.cellLike.stochastic

StochasticSimulator(Psystem) - Constructor for class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator

Constructor.

StochasticSimulator.Reaction - Class in org.gcn.plinguacore.simulator.cellLike.stochastic

Class Reaction

StochasticSimulator.Reaction(IRule) - Constructor for class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator.Reaction

StochasticTester - Class in org.gcn.plinguacore.simulator.cellLike.stochastic

Clase StochasticTester

StochasticTester(double, int, int, ISimulator) - Constructor for class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticTester

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

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

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

Stops the current thread where the run process takes place

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

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

StringReaderWrapper - Class in org.gcn.plinguacore.parser.input.byteCounter

This class provides a wrapper for StringReader which implements IByteCounter

StringReaderWrapper(StringReader) - Constructor for class org.gcn.plinguacore.parser.input.byteCounter.StringReaderWrapper

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

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

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

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

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

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

subtraction(Collection<?>) - Method in interface org.gcn.plinguacore.util.MultiSet

Subtraction between multisets

subtraction(Collection<?>, long) - Method in interface org.gcn.plinguacore.util.MultiSet

subtracts the objects in objects a number of times equal to multiplicity

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

supportsAlternateSteps() - Method in class org.gcn.plinguacore.simulator.AlternativeStepsSupportedSimulator

In AlternativeStepsSupportedSimulator instances, this method always returns true

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

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

Reports if the simulator supports alternate steps

supportsAlternativeStep(String) - Method in class org.gcn.plinguacore.simulator.CreateSimulator

Returns a boolean representing if the simulator related to id could be created capable of performing alternative steps

supportsAlternativeStep() - Method in class org.gcn.plinguacore.simulator.CreateSimulator

Returns a boolean representing if the default simulator could be created capable of performing alternative steps

supportsAlternativeStep(String) - Method in class org.gcn.plinguacore.util.psystem.Psystem

Returns a boolean representing if the simulator related to id could be created capable of performing alternative steps

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

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

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

Reports if the simulator supports step back

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

Returns true, because StepBackSupportedSimulator supports step back

swap(IndexedPriorityQueue<E>.Node<E>, IndexedPriorityQueue<E>.Node<E>) - Method in class org.gcn.plinguacore.util.IndexedPriorityQueue

Swaps the tree nodes a and b and updates the index structure properly

SwitchTo(int) - Method in class org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserTokenManager

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

This class tests if the outer multiset in the left hand of the rule is equal to the multiset into the outer membrane of the right hand of the rule, and vice versa (only if the rule is not a division, creation or dissolution rule)

SymmetricCommunication() - Constructor for class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.SymmetricCommunication

Creates a new SimetricCommunication instance, which checks only the restrictions defined on itself.

SymmetricCommunication(CheckRule) - Constructor for class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.SymmetricCommunication

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

SymportAntiportPsystemFactory - Class in org.gcn.plinguacore.simulator.cellLike.transition

This class is intended to give support for P-systems in which only membrane communication is allowed