Serialized Form

Package org.gcn.plinguacore.parser.input.plingua

Class org.gcn.plinguacore.parser.input.plingua.ParseException extends java.lang.Exception implements Serializable

serialVersionUID: 5219206325178187392L

Serialized Fields

specialConstructor

boolean specialConstructor

This variable determines which constructor was used to create this object and thereby affects the semantics of the "getMessage" method (see below).

currentToken

org.gcn.plinguacore.parser.input.plingua.Token currentToken

This is the last token that has been consumed successfully. If this object has been created due to a parse error, the token followng this token will (therefore) be the first error token.

expectedTokenSequences

int[][] expectedTokenSequences

Each entry in this array is an array of integers. Each array of integers represents a sequence of tokens (by their ordinal values) that is expected at this point of the parse.

tokenImage

java.lang.String[] tokenImage

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred. This array is defined in the generated ...Constants interface.

eol

java.lang.String eol

The end of line string for this machine.

Class org.gcn.plinguacore.parser.input.plingua.PlinguaSemanticsException extends ParseException implements Serializable

serialVersionUID: -4750534933505868248L

Serialized Fields

error

InputParserMsg error

Package org.gcn.plinguacore.simulator

Class org.gcn.plinguacore.simulator.AbstractSelectionExecutionSimulator extends AbstractSimulator implements Serializable

serialVersionUID: 1997974622465213429L

Serialized Fields

firstTime

boolean firstTime

selectedRules

java.util.Map<K,V> selectedRules

Class org.gcn.plinguacore.simulator.AbstractSimulator extends java.lang.Object implements Serializable

serialVersionUID: 8223592697775323152L

Serialized Fields

currentConfig

Configuration currentConfig

stableCurrentConfig

Configuration stableCurrentConfig

time

boolean time

verbosity

int verbosity

date

java.util.Date date

Class org.gcn.plinguacore.simulator.AlternativeStepsSupportedSimulator extends DecoratorSimulator implements Serializable

serialVersionUID: 4933648667083874575L

Class org.gcn.plinguacore.simulator.DecoratorSimulator extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

decorated

ISimulator decorated

Class org.gcn.plinguacore.simulator.ElementFileStream extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

element

java.lang.Object element

outputStream

java.io.ObjectOutputStream outputStream

inputStream

java.io.ObjectInputStream inputStream

fileRoute

java.lang.String fileRoute

Class org.gcn.plinguacore.simulator.StepBackSupportedSimulator extends DecoratorSimulator implements Serializable

serialVersionUID: -6761190875799266639L

Serialized Fields

configurationStack

java.util.Stack<E> configurationStack

Package org.gcn.plinguacore.simulator.cellLike

Class org.gcn.plinguacore.simulator.cellLike.CellLikeSimulator extends AbstractSelectionExecutionSimulator implements Serializable

serialVersionUID: 2539727644482041974L

Package org.gcn.plinguacore.simulator.cellLike.activeMembranes

Class org.gcn.plinguacore.simulator.cellLike.activeMembranes.ActiveMembranesSimulator extends CellLikeSimulator implements Serializable

serialVersionUID: -7363771600223333693L

Serialized Fields

initialConfig

boolean initialConfig

onlyEvolutionPermitted

java.util.Set<E> onlyEvolutionPermitted

Package org.gcn.plinguacore.simulator.cellLike.probabilistic

Class org.gcn.plinguacore.simulator.cellLike.probabilistic.AbstractProbabilisticSimulator extends CellLikeSimulator implements Serializable

serialVersionUID: 917064514139461645L

Class org.gcn.plinguacore.simulator.cellLike.probabilistic.BinomialProbabilisticSimulator extends AbstractProbabilisticSimulator implements Serializable

serialVersionUID: -8850790290242455072L

Serialized Fields

activations

java.util.Map<K,V> activations

binomial

cern.jet.random.Binomial binomial

Class org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticSimulator extends AbstractProbabilisticSimulator implements Serializable

serialVersionUID: -7427347014964937489L

Serialized Fields

probabilities

java.util.Map<K,V> probabilities

Package org.gcn.plinguacore.simulator.cellLike.stochastic

Class org.gcn.plinguacore.simulator.cellLike.stochastic.DeterministicWaitingTimesSimulator extends StochasticSimulator implements Serializable

serialVersionUID: 5072278426632772554L

Serialized Fields

nextTime

double nextTime

nextReaction

StochasticSimulator.Reaction nextReaction

G

java.util.List<E>[] G

P

java.util.Map<K,V> P

Class org.gcn.plinguacore.simulator.cellLike.stochastic.DirectStochasticSimulator extends StochasticSimulator implements Serializable

serialVersionUID: 3270787660596924883L

Serialized Fields

nextTime

double nextTime

Class org.gcn.plinguacore.simulator.cellLike.stochastic.EfficientStochasticSimulator extends StochasticSimulator implements Serializable

serialVersionUID: 3270787660596924883L

Serialized Fields

nextTime

double nextTime

nextReaction

StochasticSimulator.Reaction nextReaction

G

java.util.List<E>[] G

P

java.util.Map<K,V> P

seed

long seed

Class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator extends AbstractSimulator implements Serializable

serialVersionUID: 1519762430296909262L

Serialized Fields

timeOut

double timeOut

reactions

java.util.List<E> reactions

t

double t

T

double T

numberOfSteps

int numberOfSteps

variables

java.util.Map<K,V> variables

Class org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator.Reaction extends java.lang.Object implements Serializable

serialVersionUID: 5501749731967766458L

Serialized Fields

a

double a

c

double c

tau

double tau

index

int index

globalIndex

int globalIndex

rule

IRule rule

membrane

CellLikeMembrane membrane

parentMembrane

CellLikeMembrane parentMembrane

t_1

double t_1

a_before_zero

double a_before_zero

reactants

java.util.Map<K,V> reactants

outerReactants

java.util.Map<K,V> outerReactants

products

java.util.Set<E> products

outerProducts

java.util.Set<E> outerProducts

Package org.gcn.plinguacore.simulator.cellLike.transition

Class org.gcn.plinguacore.simulator.cellLike.transition.NonDeterministicTransitionSimulator extends CellLikeSimulator implements Serializable

serialVersionUID: 290211051490843577L

Class org.gcn.plinguacore.simulator.cellLike.transition.TransitionSimulator extends CellLikeSimulator implements Serializable

serialVersionUID: 5914531846669504917L

Package org.gcn.plinguacore.simulator.tissueLike

Class org.gcn.plinguacore.simulator.tissueLike.TissueLikeSimulator extends AbstractSelectionExecutionSimulator implements Serializable

serialVersionUID: -1556761252509150318L

Serialized Fields

state

int state

communications

java.util.List<E> communications

membranesToCommunicate

java.util.Set<E> membranesToCommunicate

membranesToDivide

java.util.Map<K,V> membranesToDivide

Package org.gcn.plinguacore.util

Class org.gcn.plinguacore.util.HashInfiniteMultiSet extends HashMultiSet<E> implements Serializable

serialVersionUID: -6023263700543581160L

Serialized Fields

infiniteObjects

java.util.Set<E> infiniteObjects

Class org.gcn.plinguacore.util.HashMultiSet extends java.lang.Object implements Serializable

serialVersionUID: 4265738367398769859L

Serialized Fields

entrySet

org.gcn.plinguacore.util.HashMultiSet.EntrySet entrySet

Class org.gcn.plinguacore.util.IndexedPriorityQueue extends java.lang.Object implements Serializable

serialVersionUID: -7262509096684905459L

Serialized Fields

indexes

IndexedPriorityQueue.Node<T extends E>[] indexes

root

IndexedPriorityQueue.Node<T extends E> root

Class org.gcn.plinguacore.util.IndexedPriorityQueue.Node extends java.lang.Object implements Serializable

Serialized Fields

i

int i

value

java.lang.Comparable<T> value

parent

IndexedPriorityQueue.Node<T extends E> parent

rightChild

IndexedPriorityQueue.Node<T extends E> rightChild

leftChild

IndexedPriorityQueue.Node<T extends E> leftChild

Class org.gcn.plinguacore.util.InmutableMultiSet extends java.lang.Object implements Serializable

serialVersionUID: 3690031173844421012L

Serialized Fields

multiset

MultiSet<E> multiset

Class org.gcn.plinguacore.util.Pair extends java.lang.Object implements Serializable

Serialized Fields

first

java.lang.Object first

second

java.lang.Object second

Class org.gcn.plinguacore.util.PlinguaCoreException extends java.lang.Exception implements Serializable

serialVersionUID: -3663466397732576408L

Class org.gcn.plinguacore.util.PlinguaPanicError extends java.lang.Error implements Serializable

serialVersionUID: 8851024763551280228L

Class org.gcn.plinguacore.util.RandomArrayList extends java.util.ArrayList<E> implements Serializable

serialVersionUID: 6028247731361474736L

Class org.gcn.plinguacore.util.RandomNumbersGenerator extends cern.jet.random.engine.MersenneTwister implements Serializable

serialVersionUID: -2655083177269543028L

Class org.gcn.plinguacore.util.Triple extends Pair<E,T> implements Serializable

Serialized Fields

third

java.lang.Object third

Package org.gcn.plinguacore.util.check

Class org.gcn.plinguacore.util.check.BaseCheck extends java.lang.Object implements Serializable

serialVersionUID: -3685134922361847876L

Serialized Fields

causes

java.util.List<E> causes

initializedCauses

boolean initializedCauses

Class org.gcn.plinguacore.util.check.DecoratorCheck extends java.lang.Object implements Serializable

serialVersionUID: 339922718160092202L

Serialized Fields

decorated

org.gcn.plinguacore.util.check.InnerCheck<T> decorated

Package org.gcn.plinguacore.util.psystem

Class org.gcn.plinguacore.util.psystem.AlphabetObject extends java.lang.Object implements Serializable

serialVersionUID: 4367150243594694785L

Serialized Fields

name

java.lang.String name

indexes

int[] indexes

strObj

java.lang.String strObj

Class org.gcn.plinguacore.util.psystem.Configuration extends java.lang.Object implements Serializable

serialVersionUID: -6642873032924795615L

Serialized Fields

membraneStructure

MembraneStructure membraneStructure

number

int number

psystem

Psystem psystem

Class org.gcn.plinguacore.util.psystem.Label extends java.lang.Object implements Serializable

serialVersionUID: 382343707864922136L

Serialized Fields

labelID

java.lang.String labelID

environmentID

java.lang.String environmentID

Class org.gcn.plinguacore.util.psystem.Psystem extends java.lang.Object implements Serializable

serialVersionUID: 3801859310721771797L

Serialized Fields

rules

RulesSet rules

alphabet

java.util.SortedSet<E> alphabet

initialMultiSets

java.util.Map<K,V> initialMultiSets

membraneStructure

MembraneStructure membraneStructure

Package org.gcn.plinguacore.util.psystem.cellLike

Class org.gcn.plinguacore.util.psystem.cellLike.CellLikeConfiguration extends Configuration implements Serializable

serialVersionUID: 5324665255482026462L

Serialized Fields

environment

MultiSet<E> environment

Class org.gcn.plinguacore.util.psystem.cellLike.CellLikePsystem extends Psystem implements Serializable

serialVersionUID: 8332316133669389557L

Package org.gcn.plinguacore.util.psystem.cellLike.membrane

Class org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeMembrane extends ChangeableMembrane implements Serializable

serialVersionUID: -6142935731109264452L

Serialized Fields

childMembranes

java.util.List<E> childMembranes

Class org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeNoSkinMembrane extends CellLikeMembrane implements Serializable

serialVersionUID: 1L

Serialized Fields

skinMembrane

CellLikeSkinMembrane skinMembrane

parentMembrane

CellLikeMembrane parentMembrane

Class org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeSkinMembrane extends CellLikeMembrane implements Serializable

serialVersionUID: 1L

Serialized Fields

nextId

int nextId

Package org.gcn.plinguacore.util.psystem.checkPsystem

Class org.gcn.plinguacore.util.psystem.checkPsystem.BaseCheckPsystem extends BaseCheck<Psystem> implements Serializable

serialVersionUID: -6066387104689946842L

Class org.gcn.plinguacore.util.psystem.checkPsystem.DecoratorCheckPsystem extends DecoratorCheck<Psystem> implements Serializable

serialVersionUID: 3886333432897639782L

Package org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem

Class org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem.CompleteProbabilities extends DecoratorCheckPsystem implements Serializable

serialVersionUID: -8921870457272723574L

Serialized Fields

causeRules

java.util.List<E> causeRules

Class org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem.ConsistentRules extends DecoratorCheckPsystem implements Serializable

serialVersionUID: -3213988448397373493L

Serialized Fields

causeRules

java.util.List<E> causeRules

Package org.gcn.plinguacore.util.psystem.membrane

Class org.gcn.plinguacore.util.psystem.membrane.ChangeableMembrane extends Membrane implements Serializable

serialVersionUID: -8308332619574555993L

Serialized Fields

id

int id

Class org.gcn.plinguacore.util.psystem.membrane.Membrane extends java.lang.Object implements Serializable

serialVersionUID: 979202030107031549L

Serialized Fields

multiSet

MultiSet<E> multiSet

label

Label label

charge

byte charge

Package org.gcn.plinguacore.util.psystem.rule

Class org.gcn.plinguacore.util.psystem.rule.AbstractRule extends java.lang.Object implements Serializable

serialVersionUID: -2223028108798909376L

Serialized Fields

handCorrespondence

InnerRuleMembrane[] handCorrespondence

dissolves

boolean dissolves

leftHandRule

LeftHandRule leftHandRule

rightHandRule

RightHandRule rightHandRule

newMembranes

java.util.List<E> newMembranes

Class org.gcn.plinguacore.util.psystem.rule.HandRule extends java.lang.Object implements Serializable

serialVersionUID: 5525186671845193265L

Serialized Fields

multiset

MultiSet<E> multiset

outerMembrane

OuterRuleMembrane outerMembrane

Class org.gcn.plinguacore.util.psystem.rule.InnerRuleMembrane extends Membrane implements Serializable

serialVersionUID: -4060305358392778861L

Class org.gcn.plinguacore.util.psystem.rule.LeftHandRule extends HandRule implements Serializable

serialVersionUID: 931919701324713064L

Class org.gcn.plinguacore.util.psystem.rule.OuterRuleMembrane extends Membrane implements Serializable

serialVersionUID: 6694799090774398321L

Serialized Fields

innerMembranes

java.util.List<E> innerMembranes

Class org.gcn.plinguacore.util.psystem.rule.RightHandRule extends HandRule implements Serializable

serialVersionUID: 4916985606491545835L

Serialized Fields

secondOuterMembrane

OuterRuleMembrane secondOuterMembrane

Class org.gcn.plinguacore.util.psystem.rule.RulesSet extends java.lang.Object implements Serializable

serialVersionUID: 244011999390422931L

Serialized Fields

checkRule

CheckRule checkRule

rules

java.util.Map<K,V> rules

rulesByEnv

java.util.Map<K,V> rulesByEnv

allRules

java.util.Set<E> allRules

alphabet

java.util.SortedSet<E> alphabet

Package org.gcn.plinguacore.util.psystem.rule.checkRule

Class org.gcn.plinguacore.util.psystem.rule.checkRule.DecoratorCheckRule extends java.lang.Object implements Serializable

serialVersionUID: 339922718160092202L

Serialized Fields

decorated

org.gcn.plinguacore.util.psystem.rule.checkRule.InnerCheckRule decorated

Package org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.Constant extends NoConstant implements Serializable

serialVersionUID: -165317059971834710L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoCharges extends DecoratorCheckRule implements Serializable

serialVersionUID: 5023790016455964242L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoConstant extends DecoratorCheckRule implements Serializable

serialVersionUID: -2136701933336259351L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoCooperation extends DecoratorCheckRule implements Serializable

serialVersionUID: -6167535217122687596L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoCooperationWithDivision extends DecoratorCheckRule implements Serializable

serialVersionUID: 9147605245125836526L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoCreation extends DecoratorCheckRule implements Serializable

serialVersionUID: -4964414927791023114L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoDifferentMainLabels extends DecoratorCheckRule implements Serializable

serialVersionUID: -2799599828518072462L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoDissolution extends DecoratorCheckRule implements Serializable

serialVersionUID: -3122646462770471407L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoDivision extends DecoratorCheckRule implements Serializable

serialVersionUID: -2822148379585645980L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoEmptyLeftMultiSet extends DecoratorCheckRule implements Serializable

serialVersionUID: 2521796773673522199L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoEvolution extends DecoratorCheckRule implements Serializable

serialVersionUID: 9147605245125836526L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoGeneStrings extends DecoratorCheckRule implements Serializable

serialVersionUID: -4702673900938431959L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftExternalMultiSet extends DecoratorCheckRule implements Serializable

serialVersionUID: -2202497668908299011L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftExternalMultiSetWithCreation extends org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.AbstractNoLeftExternalMultiSet implements Serializable

serialVersionUID: 752298869777105644L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftExternalMultiSetWithDissolution extends org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.AbstractNoLeftExternalMultiSet implements Serializable

serialVersionUID: -5110347715619492401L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftExternalMultiSetWithDivision extends org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.AbstractNoLeftExternalMultiSet implements Serializable

serialVersionUID: -7846584198238362209L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftInnerMembranes extends DecoratorCheckRule implements Serializable

serialVersionUID: 1387261979751334794L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftRepeatedLabels extends NoRepeatedLabels implements Serializable

serialVersionUID: 2814803775414901272L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoMultipleProduction extends DecoratorCheckRule implements Serializable

serialVersionUID: -2863456471230961641L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoMultipleProductionWithDivision extends DecoratorCheckRule implements Serializable

serialVersionUID: 9147605245125836526L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoPriority extends DecoratorCheckRule implements Serializable

serialVersionUID: -8215412423729798727L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoRepeatedLabels extends DecoratorCheckRule implements Serializable

serialVersionUID: -8267221205826990188L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoRightExternalMultiSet extends DecoratorCheckRule implements Serializable

serialVersionUID: -4619746450626196505L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoRightInnerMembranes extends DecoratorCheckRule implements Serializable

serialVersionUID: 2353523152452738877L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoRightRepeatedLabels extends NoRepeatedLabels implements Serializable

serialVersionUID: 6671029857387676280L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NotAllEmptyMultiSet extends DecoratorCheckRule implements Serializable

serialVersionUID: -3963693050501443891L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.Ratio extends Constant implements Serializable

serialVersionUID: 2198306913397498983L

Class org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.SymmetricCommunication extends DecoratorCheckRule implements Serializable

serialVersionUID: 8634047200621525016L

Package org.gcn.plinguacore.util.psystem.rule.tissueLike

Class org.gcn.plinguacore.util.psystem.rule.tissueLike.DoubleCommunicationTissueLikeRule extends TissueLikeRule implements Serializable

serialVersionUID: 5601163359552027963L

Serialized Fields

communications

java.util.List<E> communications

executions

long executions

Class org.gcn.plinguacore.util.psystem.rule.tissueLike.TissueLikeRule extends AbstractRule implements Serializable

serialVersionUID: -2311858756048522881L

Package org.gcn.plinguacore.util.psystem.tissueLike

Class org.gcn.plinguacore.util.psystem.tissueLike.TissueLikeConfiguration extends Configuration implements Serializable

serialVersionUID: 1762892867128733623L

Class org.gcn.plinguacore.util.psystem.tissueLike.TissueLikePsystem extends Psystem implements Serializable

serialVersionUID: 2290929626246752890L

Package org.gcn.plinguacore.util.psystem.tissueLike.membrane

Class org.gcn.plinguacore.util.psystem.tissueLike.membrane.TissueLikeEnvironment extends TissueLikeMembrane implements Serializable

serialVersionUID: -9069058949375353260L

Class org.gcn.plinguacore.util.psystem.tissueLike.membrane.TissueLikeMembrane extends ChangeableMembrane implements Serializable

serialVersionUID: 4331622171073550025L

Serialized Fields

structure

TissueLikeMembraneStructure structure