A B C D E F G H I K L M N O P 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

GENERIC_ENVIRONMENT - Static variable in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMethods

GeneString - Class in org.gcn.plinguacore.util

Class to handle strings in P-systems.

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

get(Object) - Method in class org.gcn.plinguacore.util.ExtendedLinkedHashSet

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

Gets the current AbstractPsystemFactory instance

getAccuracy(long) - Static method in class org.gcn.plinguacore.util.ByteOrderDataOutputStream

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.spiking.membrane.SpikingMembraneStructure

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

getAllZeroes() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.DynamicMatrix

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

getArcInfo(Integer, Integer) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getArcs() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.Astrocyte

getAstrocyte(String) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getAstrocyteArcs(String) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getAstrocyteCtrlArcs(String) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getAstrocyteCtrlList() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.ArcInfo

getAstrocyteFunction(String) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getAstrocyteList() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.ArcInfo

getAstType() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.ArcInfo

getAsynch() - Method in class org.gcn.plinguacore.simulator.spiking.SpikingSimulator

getAsynchMode() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getAsynchValidConfiguration() - Method in class org.gcn.plinguacore.simulator.spiking.SpikingSimulator

getAsynchValidConfiguration() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

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

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

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

Gets the line at which the message begins

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

getBinarySpikeTrain() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingEnvironment

getBuddingDivision() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane

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

getCellById(int) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

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

getCellsByLabel(String) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

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

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

Deprecated.

getColumn() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixKey

getColumns() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMatrix

getColumns() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.DndpMatrix

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.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.spiking.SpikingPsystemFactory

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

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

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

getCtrlArcs() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.BinderAstrocyte

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

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

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

getDelay() - Method in class org.gcn.plinguacore.util.psystem.rule.spiking.SpikingRule

getDictionary() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getDynamicMatrix() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.DCBAProbabilisticSimulator

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

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

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

Gets the line at which the message ends

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

getEnvironment() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentLeftHandRule

getEnvironment(IRule) - Static method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMethods

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.spiking.membrane.SpikingMembraneStructure

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

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.spiking.membrane.SpikingMembraneStructure

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

getEnvironmentLabels() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMatrix

getEnvironmentLeftHandRule() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentRulesBlock

getEnvironmentMembrane() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getEnvironmentRightHandRules() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentRulesBlock

getEnvironments(CellLikeSkinMembrane) - Static method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMethods

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

getExecutionResult() - Method in class org.gcn.plinguacore.simulator.spiking.SpikingSimulator

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

getFilterColumns() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.DynamicMatrix

getFilterColumsIterator() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.DndpMatrix

getFilterRows() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.DynamicMatrix

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

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

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

getHandRuleSpikingStringSize(HandRule) - Method in class org.gcn.plinguacore.util.psystem.rule.spiking.SpikingRule

getId() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.HashKey

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

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

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

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

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

getInhibited() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.ArcInfo

getInhibitory() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.ArcInfo

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

getInputMembrane() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getInputSequence() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingEnvironment

getInputSequenceValue(long) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingEnvironment

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.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.spiking.SpikingPsystemFactory

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

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

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

getK() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.AbstractDnd2Sim

getLabel() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixRow

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

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

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

getLeftHandRuleObjects(Map<String, String>) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentRulesBlock

getLeftHandRuleObjects(Map<String, String>) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixColumn

getLeftHandRuleObjects(Map<String, String>) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonRulesBlock

getLeftHandRuleSpikingString() - Method in class org.gcn.plinguacore.util.psystem.rule.spiking.SpikingRule

getLeftHandRuleSpikingStringSize() - Method in class org.gcn.plinguacore.util.psystem.rule.spiking.SpikingRule

getLFunctionNames() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.Astrocyte

getLhr() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.HashKey

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

Deprecated.

getLThresholds() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.Astrocyte

getMainLabel() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentRulesBlock

getMainLabel() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixColumn

getMainLabel() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonRulesBlock

getMainMembraneCharge() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonHandRule

getMainMembraneCharge() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticLeftHandRule

getMainMembraneEnvironment() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticLeftHandRule

getMainMembraneId() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticLeftHandRule

getMainMembraneLabel() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonLeftHandRule

getMainMembraneLabel() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticLeftHandRule

getMainMembraneMultiSet() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticLeftHandRule

getMainMultiSet() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonHandRule

getMatrix() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.DndpMatrix

getMaximunByLeftHandRule(ProbabilisticLeftHandRule) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.DndpMatrix

getMaxIterations() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.AbstractDndProbabilisticSimulator

getMaxIterations() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.Dnd4ProbabilisticSimulator

getMaxIterations() - Method in interface org.gcn.plinguacore.simulator.cellLike.probabilistic.ISelectionLoopAlgorithm

getMembrane(String, String, CellLikeSkinMembrane, Map<String, Integer>) - Static method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMethods

getMembrane(int) - Method in class org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeSkinMembrane

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

getMembrane(int) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

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

getMembraneIdsByLabelAndEnvironment(CellLikeSkinMembrane) - Static method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMethods

getMembraneSpikingString() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane

getMembraneSpikingStringSize() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane

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

getMin() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixColumn

getMinimunByLeftHandRule(ProbabilisticLeftHandRule) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.DndpMatrix

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

getNaturalSpikeTrain() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingEnvironment

getNewObjects() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentRightHandRule

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

getNumberOfRules(String, String, int) - Method in class org.gcn.plinguacore.util.psystem.rule.RulesSet

getNumParams() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.AstrocyteFunction

getNumParams() - Method in interface org.gcn.plinguacore.util.psystem.spiking.membrane.EvaluableFunction

getObject() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentLeftHandRule

getObject() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixRow

getObject() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.HashKey

getObject() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane

getObject(Membrane) - Static method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane

getObjectCount() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane

getObjectCount(Membrane) - Static method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane

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

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

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

getOutputMembranes() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

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

getParentMembraneMultiSet() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticLeftHandRule

getParentMultiSet() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonHandRule

getParents(CellLikeMembrane, Map<String, String>) - Static method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMethods

getParents(CellLikeMembrane) - Static method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMethods

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

Return general information about available parsers

getPotential() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.Astrocyte

getPredecessors(SpikingMembrane) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

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

getProbability(String) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentRightHandRule

getProbability(String) - Method in interface org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.IRightHandRule

getProbability(String) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonRightHandRule

getProbability(IRule) - Static method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMethods

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

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

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

getrCharge() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonRulesBlock

getRegExp() - Method in class org.gcn.plinguacore.util.psystem.rule.spiking.SpikingRule

getReglas() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.ParteIzquierda

Deprecated.

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

Gets the report map of the last parsing

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

getRightHandRules() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentRulesBlock

getRightHandRules() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixColumn

getRightHandRules() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonRulesBlock

getRightHandRuleSpikingStringSize() - Method in class org.gcn.plinguacore.util.psystem.rule.spiking.SpikingRule

getRow() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.MatrixKey

getRows() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMatrix

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

getRuleId(String) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.EnvironmentRightHandRule

getRuleId(String) - Method in interface org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.IRightHandRule

getRuleId(String) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonRightHandRule

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

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

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

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

getRulesByLeftHandRuleIterator(ProbabilisticLeftHandRule) - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.DndpMatrix

getRulesMap() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.DndProbabilisticSelExecThread

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

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

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

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

Gets the second outer rule membrane if it exists.

getSelectedRule() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane

getSelectedRules() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.DynamicMatrix

getSequential() - Method in class org.gcn.plinguacore.simulator.spiking.SpikingSimulator

getSequentialMode() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getShowBinarySequence() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getShowNaturalSequence() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

getShowSummatories() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

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

getSkeletonLeftHandRule() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.SkeletonRulesBlock

getSourceId() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.ArcInfo

getSpikes() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.Astrocyte

getSpikesInput() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.ArcInfo

getSpikesOutput() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.ArcInfo

getStaticMatrix() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.DCBAProbabilisticSimulator

getStaticMatrix() - Method in class org.gcn.plinguacore.simulator.cellLike.probabilistic.dcba.StaticMatrix

getStepsTaken() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingEnvironment

getStepsToOpen() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane

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

getStructure() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.Astrocyte

getStructure() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembrane

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

getSuccessors(SpikingMembrane) - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.SpikingMembraneStructure

GetSuffix(int) - Method in class org.gcn.plinguacore.parser.input.plingua.SimpleCharStream

getTargetId() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.ArcInfo

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

getType() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.Astrocyte

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

getWeight() - Method in class org.gcn.plinguacore.util.psystem.spiking.membrane.ArcInfo

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