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

C

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

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

CellLikeConfiguration - Class in org.gcn.plinguacore.util.psystem.cellLike

This class represents configurations in cell-like P-systems

CellLikeMembrane - Class in org.gcn.plinguacore.util.psystem.cellLike.membrane

A class for a membrane for cell-like P systems

CellLikeMembraneFactory - Class in org.gcn.plinguacore.util.psystem.cellLike.membrane

This class creates CellLikeMembrane instances, according to Simple Factory idiom

CellLikeMembraneFactory() - Constructor for class org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeMembraneFactory

CellLikeNoSkinMembrane - Class in org.gcn.plinguacore.util.psystem.cellLike.membrane

This class represents cell-like membranes which are not skin membranes

CellLikePsystem - Class in org.gcn.plinguacore.util.psystem.cellLike

This class represents P-systems belonging to cell-like group

CellLikePsystem() - Constructor for class org.gcn.plinguacore.util.psystem.cellLike.CellLikePsystem

Creates a new P-system without skin membrane

CellLikeRuleFactory - Class in org.gcn.plinguacore.util.psystem.rule.cellLike

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

CellLikeSimulator - Class in org.gcn.plinguacore.simulator.cellLike

A simulator for cell-like P systems

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

CellLikeSkinMembrane - Class in org.gcn.plinguacore.util.psystem.cellLike.membrane

This class represents cell-like skin membranes

ChangeableMembrane - Class in org.gcn.plinguacore.util.psystem.membrane

This class provides methods for modifiable membranes

ChangeableMembrane(Label, byte, MultiSet<String>) - Constructor for class org.gcn.plinguacore.util.psystem.membrane.ChangeableMembrane

ChangeableMembrane(Label, byte) - Constructor for class org.gcn.plinguacore.util.psystem.membrane.ChangeableMembrane

Creates a new ChangeableMembrane instance

ChangeableMembrane(Label) - Constructor for class org.gcn.plinguacore.util.psystem.membrane.ChangeableMembrane

Creates a new ChangeableMembrane instance which charge is 0

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

Check<T> - Interface in org.gcn.plinguacore.util.check

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

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

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

CheckPsystem - Interface in org.gcn.plinguacore.util.psystem.checkPsystem

checkPsystem(Psystem) - Method in interface org.gcn.plinguacore.util.psystem.checkPsystem.CheckPsystem

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

CheckRule - Interface in org.gcn.plinguacore.util.psystem.rule.checkRule

This interface defines all the functionality to test if a rule complies with all the conditions stated by a model

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

Checks if the rule r fulfills the terms stated

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

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

Returns true if the IRule passed as argument complies the model conditions

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

Returns true if all the rules within the RuleSet complies the model conditions

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

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

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

Cleans the configurations previously reached

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Communication - Class in org.gcn.plinguacore.util.psystem.rule.tissueLike

Communication(TissueLikeMembrane, TissueLikeMembrane, DoubleCommunicationTissueLikeRule, long) - Constructor for class org.gcn.plinguacore.util.psystem.rule.tissueLike.Communication

compare(IRule, IRule) - Method in class org.gcn.plinguacore.util.psystem.rule.RuleComparator

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

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

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

CompleteProbabilities - Class in org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem

CompleteProbabilities() - Constructor for class org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem.CompleteProbabilities

CompleteProbabilities(CheckPsystem) - Constructor for class org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem.CompleteProbabilities

Configuration - Class in org.gcn.plinguacore.util.psystem

An abstract class for a Configuration

ConsistentRules - Class in org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem

ConsistentRules() - Constructor for class org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem.ConsistentRules

ConsistentRules(CheckPsystem) - Constructor for class org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem.ConsistentRules

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

This class tests if the rule holds a ratio or kinetic constant.

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

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

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

Creates a new Constant instance, which wraps cr as stated by decorator pattern.

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

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

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

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

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

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

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

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

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

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

count(MultiSet<String>) - Method in class org.gcn.plinguacore.util.GeneString

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

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

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

count(Object) - Method in interface org.gcn.plinguacore.util.MultiSet

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

Counts the number of alternate steps to take

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

If possible, counts the number of alternative steps available for the simulator

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

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

Counts the alternative steps which could be taken

countBytes(int, int) - Method in interface org.gcn.plinguacore.parser.input.byteCounter.IByteCounter

This method counts the number of bytes from the beginning of a file at position [line,column]

countBytes(int, int) - Method in class org.gcn.plinguacore.parser.input.byteCounter.InputStreamWrapper

countBytes(int, int) - Method in class org.gcn.plinguacore.parser.input.byteCounter.StringReaderWrapper

countExecutions(ChangeableMembrane, MultiSet<String>) - Method in interface org.gcn.plinguacore.util.psystem.rule.IRule

Counts the number of possible executions of the current rule on a membrane

countExecutions(ChangeableMembrane, MultiSet<String>) - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.DoubleCommunicationTissueLikeRule

countExecutions(ChangeableMembrane, MultiSet<String>) - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.TissueLikeRule

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

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

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

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

counts the number of subsets

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

Creates an AbstractPsystemFactory instance according to the model name given

createBasicRule(boolean, LeftHandRule, RightHandRule) - Method in interface org.gcn.plinguacore.util.psystem.rule.AbstractRuleFactory

createBasicRule(boolean, LeftHandRule, RightHandRule) - Method in class org.gcn.plinguacore.util.psystem.rule.cellLike.CellLikeRuleFactory

createBasicRule(boolean, LeftHandRule, RightHandRule) - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.TissueLikeRuleFactory

createConstantRule(boolean, LeftHandRule, RightHandRule, float) - Method in interface org.gcn.plinguacore.util.psystem.rule.AbstractRuleFactory

createConstantRule(boolean, LeftHandRule, RightHandRule, float) - Method in class org.gcn.plinguacore.util.psystem.rule.cellLike.CellLikeRuleFactory

createConstantRule(boolean, LeftHandRule, RightHandRule, float) - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.TissueLikeRuleFactory

createDoubleCommunicationRule(boolean, LeftHandRule, RightHandRule) - Method in interface org.gcn.plinguacore.util.psystem.rule.AbstractRuleFactory

createDoubleCommunicationRule(boolean, LeftHandRule, RightHandRule) - Method in class org.gcn.plinguacore.util.psystem.rule.cellLike.CellLikeRuleFactory

createDoubleCommunicationRule(boolean, LeftHandRule, RightHandRule) - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.TissueLikeRuleFactory

createInfoMessage(String, int) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createInfoMessage(String, MsgInterval, int) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createInfoMessage(String, String, MsgInterval, int) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createInfoMessage(String, String, int) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createInputParserThroughExtension(String) - Method in class org.gcn.plinguacore.parser.AbstractParserFactory

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

createInternalErrorMessage(String, MsgInterval) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createInternalErrorMessage(String, String, MsgInterval) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createInternalErrorMsg(String) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createLexicalErrorMessage(String) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createLexicalErrorMessage(String, MsgInterval) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createLexicalErrorMessage(String, String, MsgInterval) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createParser(String) - Method in class org.gcn.plinguacore.parser.AbstractParserFactory

Creates a IParser instance according to the given format

createPriorityRule(boolean, LeftHandRule, RightHandRule, int) - Method in interface org.gcn.plinguacore.util.psystem.rule.AbstractRuleFactory

createPriorityRule(boolean, LeftHandRule, RightHandRule, int) - Method in class org.gcn.plinguacore.util.psystem.rule.cellLike.CellLikeRuleFactory

createPriorityRule(boolean, LeftHandRule, RightHandRule, int) - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.TissueLikeRuleFactory

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

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

createSemanticsErrorMessage(String) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createSemanticsErrorMessage(String, MsgInterval) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createSemanticsErrorMessage(String, String, MsgInterval) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

CreateSimulator - Class in org.gcn.plinguacore.simulator

This class provides support for creating simulators according to the options defined

CreateSimulator(String) - Constructor for class org.gcn.plinguacore.simulator.CreateSimulator

Creates a new instance which creates simulators for the model indicated by its name

createSimulator(boolean, boolean, String, Psystem) - Method in class org.gcn.plinguacore.simulator.CreateSimulator

Creates a new simulator, which specific classes are identified by an ID.

createSimulator(boolean, boolean, Psystem) - Method in class org.gcn.plinguacore.simulator.CreateSimulator

Creates a new simulator.

createSimulator(boolean, boolean, String) - Method in class org.gcn.plinguacore.util.psystem.Psystem

Creates a simulator to simulate this P-system.

createSimulator(boolean, boolean) - Method in class org.gcn.plinguacore.util.psystem.Psystem

Creates a simulator to simulate this P-system.

createStochasticRule(boolean, LeftHandRule, RightHandRule, float) - Method in interface org.gcn.plinguacore.util.psystem.rule.AbstractRuleFactory

createStochasticRule(boolean, LeftHandRule, RightHandRule, float) - Method in class org.gcn.plinguacore.util.psystem.rule.cellLike.CellLikeRuleFactory

createStochasticRule(boolean, LeftHandRule, RightHandRule, float) - Method in class org.gcn.plinguacore.util.psystem.rule.tissueLike.TissueLikeRuleFactory

createSyntacticErrorMessage(String) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createSyntacticErrorMessage(String, MsgInterval) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createSyntacticErrorMessage(String, String, MsgInterval) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createWarningMessage(String) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createWarningMessage(String, MsgInterval) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createWarningMessage(String, String, MsgInterval) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

createWarningMessage(String, String) - Static method in class org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory

CreationPsystemFactory - Class in org.gcn.plinguacore.simulator.cellLike.activeMembranes

This class is intended to give support for P-systems in which only membrane creation, evolution, dissolution and communication are allowed

currentToken - Variable in exception org.gcn.plinguacore.parser.input.plingua.ParseException

This is the last token that has been consumed successfully.