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

G

GENERAL_INFO - Static variable in class org.gcn.plinguacore.parser.input.VerbosityConstants

The verbosity level for simulators which are expected to report error, warning and basic info messages no messages

generateDocument(CellLikePsystem) - Method in class org.gcn.plinguacore.parser.output.XML.XMLCellLikeOutputParser

Generates the document of a P-System

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

Generates a putative time tau for this reaction, according to an exponential distribution with parameter a

GeneString - Class in org.gcn.plinguacore.util

Class to handle strings in P-systems.

GeneString(String) - Constructor for class org.gcn.plinguacore.util.GeneString

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

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

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

Gets the current AbstractPsystemFactory instance

getActivationSets(IRule, CellLikeMembrane) - Static method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticPsystemFactory

getAllMembranes() - Method in class org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeMembrane

Gets all membranes which this instance is an ancestor to

getAllMembranes() - Method in interface org.gcn.plinguacore.util.psystem.membrane.MembraneStructure

getAllMembranes() - Method in class org.gcn.plinguacore.util.psystem.tissueLike.membrane.TissueLikeMembraneStructure

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

Returns the P-system alphabet

getAlternativeStepSupportedSimulators() - Method in interface org.gcn.plinguacore.simulator.ISimulatorClassProvider

Returns an iterator on the simulators which support alternative step

getBeginByte() - Method in class org.gcn.plinguacore.parser.input.messages.MsgInterval

getBeginColumn() - Method in class org.gcn.plinguacore.parser.input.messages.MsgInterval

Gets the column at which the message begins

getBeginLine() - Method in class org.gcn.plinguacore.parser.input.messages.MsgInterval

Gets the line at which the message begins

getCauses() - Method in class org.gcn.plinguacore.util.check.BaseCheck

getCauses() - Method in interface org.gcn.plinguacore.util.check.Check

getCauses() - Method in class org.gcn.plinguacore.util.check.DecoratorCheck

getCauses() - Method in interface org.gcn.plinguacore.util.psystem.rule.checkRule.CheckRule

Gets the conditions which the rule didn't comply with

getCauses() - Method in class org.gcn.plinguacore.util.psystem.rule.checkRule.DecoratorCheckRule

getCausesString() - Method in class org.gcn.plinguacore.util.check.BaseCheck

getCausesString() - Method in interface org.gcn.plinguacore.util.check.Check

getCausesString() - Method in class org.gcn.plinguacore.util.check.DecoratorCheck

Gets a string reporting the causes of the simulator messages

getCausesString() - Method in interface org.gcn.plinguacore.util.psystem.rule.checkRule.CheckRule

Gets a String which represent all the conditions not complied by the rule

getCausesString() - Method in class org.gcn.plinguacore.util.psystem.rule.checkRule.DecoratorCheckRule

Gets a string reporting the causes of the simulator messages

getCell(int) - Method in class org.gcn.plinguacore.util.psystem.tissueLike.membrane.TissueLikeMembraneStructure

getCellLikeMembrane(Label) - Static method in class org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeMembraneFactory

Based on Simple Factory idiom, creates a membrane which label is passed as a parameter

getCellLikeMembrane(Label, CellLikeMembrane) - Static method in class org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeMembraneFactory

Based on Simple Factory idiom, creates a membrane which parent and label are passed as parameters

getCharge() - Method in class org.gcn.plinguacore.util.psystem.membrane.Membrane

gets the membrane charge value

getChargeSymbol(byte) - Static method in class org.gcn.plinguacore.util.psystem.membrane.Membrane

returns a "+" String for positive charges, a "-" String for negative charges and a "0" String for neutral chages

getCheckPsystem() - Method in class org.gcn.plinguacore.util.psystem.factory.AbstractPsystemFactory

getCheckPsystem() - Method in interface org.gcn.plinguacore.util.psystem.factory.IPsystemFactory

getCheckRule() - Method in class org.gcn.plinguacore.util.psystem.factory.AbstractPsystemFactory

getCheckRule() - Method in interface org.gcn.plinguacore.util.psystem.factory.IPsystemFactory

Gets a CheckRule object to check if the P-system complies with the model conditions, according to the specific model to give support

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

Returns the CheckRule object for this RulesSet

getChildMembranes() - Method in class org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeMembrane

Gets all child membranes

getCommandLineOption(String) - Method in interface org.gcn.plinguacore.parser.IParsersInfo

Gets the command-line option of the format file identified by the ID passed as argument

getCommandLineOptionsIterator() - Method in interface org.gcn.plinguacore.parser.IParsersInfo

Gets an iterator on the existent command-line options

getCommunications() - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.DoubleCommunicationTissueLikeRule

getConstant() - Method in interface org.gcn.plinguacore.util.psystem.rule.IConstantRule

getCreateSimulator() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticPsystemFactory

getCreateSimulator() - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticPsystemFactory

getCreateSimulator() - Method in class org.gcn.plinguacore.simulator.cellLike.transition.EvolutionCommunicationPsystemFactory

getCreateSimulator() - Method in class org.gcn.plinguacore.simulator.cellLike.transition.EvSymportAntiportPsystemFactory

getCreateSimulator() - Method in class org.gcn.plinguacore.simulator.cellLike.transition.TransitionPsystemFactory

getCreateSimulator() - Method in class org.gcn.plinguacore.simulator.tissueLike.TissueLikePsystemFactory

getCreateSimulator() - Method in interface org.gcn.plinguacore.util.psystem.factory.IPsystemFactory

Creates a CreateSimulator instance able to create simulators for the specific model represented by this instance

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

Gets the current configuration

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

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

Gets the current configuration

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

Gets the element to be loaded

getEndByte() - Method in class org.gcn.plinguacore.parser.input.messages.MsgInterval

getEndColumn() - Method in class org.gcn.plinguacore.parser.input.messages.MsgInterval

Gets the column at which the message ends

getEndLine() - Method in class org.gcn.plinguacore.parser.input.messages.MsgInterval

Gets the line at which the message ends

getEnvironment() - Method in class org.gcn.plinguacore.util.psystem.cellLike.CellLikeConfiguration

getEnvironment() - Method in class org.gcn.plinguacore.util.psystem.Configuration

getEnvironment() - Method in class org.gcn.plinguacore.util.psystem.tissueLike.membrane.TissueLikeMembraneStructure

getEnvironment() - Method in class org.gcn.plinguacore.util.psystem.tissueLike.TissueLikeConfiguration

getEnvironmentID() - Method in class org.gcn.plinguacore.util.psystem.Label

getEnvironmentLabel() - Method in class org.gcn.plinguacore.util.psystem.tissueLike.membrane.TissueLikeMembraneStructure

getError() - Method in exception org.gcn.plinguacore.parser.input.plingua.PlinguaSemanticsException

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

Gets the errors channel

getExecutions() - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.Communication

getExtendedMsg() - Method in class org.gcn.plinguacore.parser.input.messages.InputParserAbstractMsg

getExtendedMsg() - Method in class org.gcn.plinguacore.parser.input.messages.InputParserDecoratorMsg

getExtendedMsg() - Method in interface org.gcn.plinguacore.parser.input.messages.InputParserMsg

Gets the extension of the message

getFileExtension(String) - Method in interface org.gcn.plinguacore.parser.IParsersInfo

Gets the file extension of the format identified by the ID passed as argument

getFileExtensionsIterator() - Method in interface org.gcn.plinguacore.parser.IParsersInfo

getFirst() - Method in class org.gcn.plinguacore.util.Pair

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

getFirstMembrane() - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.Communication

getFormatByCommandLineOption(String) - Method in interface org.gcn.plinguacore.parser.IParsersInfo

Gets the ID of the format file whose command-line option is passed as argument

getFormatByExtension(String) - Method in interface org.gcn.plinguacore.parser.IParsersInfo

Gets the ID of the format file whose file extension is passed as argument

getFormatsIterator() - Method in interface org.gcn.plinguacore.parser.IParsersInfo

Gets an iterator over the recognized IDs

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

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

Gets the ID of the membrane, a unique identifier for it

getIdentifiersIterator() - Method in interface org.gcn.plinguacore.simulator.ISimulatorInfo

Returns an iterator on the model identifiers

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

getIndexes() - Method in class org.gcn.plinguacore.util.psystem.AlphabetObject

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

Gets the PrintStream instance to write information

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

Gets the info channel

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

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

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

Returns the initial P-system multisets

getInnerRuleMembranes() - Method in class org.gcn.plinguacore.util.psystem.rule.OuterRuleMembrane

Gets all inner rule membranes involved in the rule

getInputFormatClassName(String) - Method in interface org.gcn.plinguacore.parser.IParsersClassProvider

Gets the name of the InputParser subclass for the format

getInputFormatClassNameThroughExtension(String) - Method in interface org.gcn.plinguacore.parser.IParsersClassProvider

Looks if there's any input format whose files correspond to the extension given and returns the name of the input format class which parses that format

getInputFormatsIterator() - Method in interface org.gcn.plinguacore.parser.IParsersInfo

Gets an iterator on the existent input formats IDs

getInstance() - Static method in class org.gcn.plinguacore.simulator.cellLike.activeMembranes.CreationPsystemFactory

Gets only instance of CreationPsystemFactory class, as stated in Singleton pattern

getInstance() - Static method in class org.gcn.plinguacore.simulator.cellLike.activeMembranes.DivisionPsystemFactory

Gets only instance of DivisionPsystemFactory class, as stated in Singleton pattern

getInstance() - Static method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticPsystemFactory

Gets the only instance of ProbabilisticPsystemFactory, according to Singleton pattern

getInstance() - Static method in class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticPsystemFactory

getInstance() - Static method in class org.gcn.plinguacore.simulator.cellLike.transition.EvolutionCommunicationPsystemFactory

getInstance() - Static method in class org.gcn.plinguacore.simulator.cellLike.transition.EvSymportAntiportPsystemFactory

Gets only instance of EvSymportAntiportPsystemFactory class, as stated in Singleton pattern

getInstance() - Static method in class org.gcn.plinguacore.simulator.cellLike.transition.SymportAntiportPsystemFactory

Gets only instance of SymportAntiportPsystemFactory class, as stated in Singleton pattern

getInstance() - Static method in class org.gcn.plinguacore.simulator.cellLike.transition.TransitionPsystemFactory

Gets only instance of TransitionPsystemFactory class, as stated in Singleton pattern

getInstance() - Static method in class org.gcn.plinguacore.simulator.tissueLike.TissueLikePsystemFactory

getInstance() - Static method in class org.gcn.plinguacore.util.RandomNumbersGenerator

getInterval() - Method in class org.gcn.plinguacore.parser.input.messages.InputParserAbstractMsg

getInterval() - Method in class org.gcn.plinguacore.parser.input.messages.InputParserDecoratorMsg

getInterval() - Method in interface org.gcn.plinguacore.parser.input.messages.InputParserMsg

Gets the message interval

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

getLabel() - Method in class org.gcn.plinguacore.util.psystem.membrane.Membrane

getLabelID() - Method in class org.gcn.plinguacore.util.psystem.Label

getLabelObj() - Method in class org.gcn.plinguacore.util.psystem.membrane.Membrane

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

getLeftHandRule() - Method in class org.gcn.plinguacore.util.psystem.rule.AbstractRule

Gets the left hand rule of the current rule

getLeftHandRule() - Method in interface org.gcn.plinguacore.util.psystem.rule.IRule

getMeans() - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticTester

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

getMembraneStructure() - Method in class org.gcn.plinguacore.util.psystem.Configuration

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

getMessage() - Method in class org.gcn.plinguacore.parser.input.messages.InputParserAbstractMsg

getMessage() - Method in class org.gcn.plinguacore.parser.input.messages.InputParserDecoratorMsg

getMessage() - Method in interface org.gcn.plinguacore.parser.input.messages.InputParserMsg

Gets the contained message

getMessage() - Method in exception org.gcn.plinguacore.parser.input.plingua.ParseException

This method has the standard behavior when this object has been created using the standard constructors.

getMessage() - Method in exception org.gcn.plinguacore.parser.input.plingua.PlinguaSemanticsException

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

Gets the model name of the Simulator

getModelClassName(String) - Method in interface org.gcn.plinguacore.util.psystem.factory.IModelsClassProvider

Gets the name of the simulator class for the model name passed

getModelId(String) - Method in interface org.gcn.plinguacore.util.psystem.factory.IModelsClassProvider

Gets the model name supported by the simulator (identified by its name) passed

getModelName() - Method in class org.gcn.plinguacore.util.psystem.factory.AbstractPsystemFactory

getModelName() - Method in interface org.gcn.plinguacore.util.psystem.factory.IPsystemFactory

Gets the name of the specific model this class gives support

getModelsInfo() - Static method in class org.gcn.plinguacore.util.psystem.factory.AbstractPsystemFactory

getModelsIterator() - Method in interface org.gcn.plinguacore.util.psystem.factory.IModelsInfo

Gets an iterator on the models supported

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

Gets the PrintStream instance to write messages

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

Gets the membrane multiset

getMultiSet() - Method in class org.gcn.plinguacore.util.psystem.membrane.Membrane

gets the membrane multiset

getMultiSet() - Method in class org.gcn.plinguacore.util.psystem.rule.HandRule

Gets the outer multiset out of all membranes

getName() - Method in class org.gcn.plinguacore.util.psystem.AlphabetObject

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

getNextReaction() - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.DirectStochasticSimulator

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

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

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

getNextTime() - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.DirectStochasticSimulator

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

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

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

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

getNumber() - Method in class org.gcn.plinguacore.util.psystem.Configuration

getNumberOfGroups() - Method in class org.gcn.plinguacore.util.GeneString

getObjects() - Method in class org.gcn.plinguacore.util.psystem.rule.AbstractRule

Gets all different objects within the rule

getObjects() - Method in class org.gcn.plinguacore.util.psystem.rule.HandRule

Returns all different objects involved in the rule

getObjects() - Method in interface org.gcn.plinguacore.util.psystem.rule.IRule

getObjects() - Method in class org.gcn.plinguacore.util.psystem.rule.RightHandRule

Gets all objects involved in the rule including those in the second membrane

getOuterRuleMembrane() - Method in class org.gcn.plinguacore.util.psystem.rule.HandRule

Gets the hand outer rule membrane

getOutputFormatClassName(String) - Method in interface org.gcn.plinguacore.parser.IParsersClassProvider

Gets the name of the OutputParser subclass for the format

getOutputFormatsIterator() - Method in interface org.gcn.plinguacore.parser.IParsersInfo

Gets an iterator on the existent output formats IDs

getParameters() - Method in class org.gcn.plinguacore.parser.input.plingua.PlinguaInputParser

getParentMembrane() - Method in class org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeNoSkinMembrane

Gets the parent membrane

getParserInfo() - Static method in class org.gcn.plinguacore.parser.AbstractParserFactory

Return general information about available parsers

getPriority() - Method in interface org.gcn.plinguacore.util.psystem.rule.IPriorityRule

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

Gets the P-system simulated

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

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

Returns the P-system simulated

getPsystem() - Method in class org.gcn.plinguacore.util.psystem.Configuration

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

Gets the report map of the last parsing

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

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

getRightHandRule() - Method in class org.gcn.plinguacore.util.psystem.rule.AbstractRule

Gets the right hand rule of the current rule

getRightHandRule() - Method in interface org.gcn.plinguacore.util.psystem.rule.IRule

getRule() - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.Communication

getRuleFactory() - Method in class org.gcn.plinguacore.util.psystem.factory.AbstractPsystemFactory

getRuleFactory() - Method in interface org.gcn.plinguacore.util.psystem.factory.IPsystemFactory

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

getRulesByActivationSet(CellLikePsystem) - Static method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticPsystemFactory

getSecond() - Method in class org.gcn.plinguacore.util.Pair

getSecondMembrane() - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.Communication

getSecondOuterRuleMembrane() - Method in class org.gcn.plinguacore.util.psystem.rule.RightHandRule

Gets the second outer rule membrane if it exists.

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

Gets an iterator on all simulators IDs

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

Gets an iterator on all possible simulators IDs for the Psystem

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

getStandarDesviations() - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticTester

getString(String) - Static method in class org.gcn.plinguacore.util.GeneString

getStructure() - Method in class org.gcn.plinguacore.util.psystem.tissueLike.membrane.TissueLikeMembrane

getT_1() - Method in class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator.Reaction

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

getThird() - Method in class org.gcn.plinguacore.util.Triple

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

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

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

Gets the elapsed time since the beginning of the simulation

getType() - Method in class org.gcn.plinguacore.parser.input.messages.InputParserDecoratorMsg

getType() - Method in interface org.gcn.plinguacore.parser.input.messages.InputParserMsg

Gets the type of the contained message

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

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

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

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

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

Gets the verbosity level

getVerbosityLevel() - Method in class org.gcn.plinguacore.parser.input.messages.InputParserDecoratorMsg

getVerbosityLevel() - Method in interface org.gcn.plinguacore.parser.input.messages.InputParserMsg

Gets the verbosity level of the message

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

Gets the PrintStream instance to write warnings

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

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