| _agentGrid | simulator.agent.SpecialisedAgent | protected |
| _agentGridIndex | simulator.agent.LocatedAgent | protected |
| _birthday | simulator.agent.Agent | protected |
| _diff | simulator.agent.LocatedAgent | protectedstatic |
| _distCumProb | simulator.agent.LocatedAgent | |
| _distProb | simulator.agent.LocatedAgent | |
| _divisionDirection | simulator.agent.LocatedAgent | protected |
| _epsSpecies | simulator.agent.zoo.Bacterium | protected |
| _family | simulator.agent.Agent | protected |
| _genealogy | simulator.agent.Agent | protected |
| _generation | simulator.agent.Agent | protected |
| _hasEps | simulator.agent.zoo.Bacterium | protected |
| _hasInert | simulator.agent.zoo.Bacterium | protected |
| _isAttached | simulator.agent.LocatedAgent | protected |
| _lastStep | simulator.agent.Agent | protected |
| _location | simulator.agent.LocatedAgent | protected |
| _movement | simulator.agent.LocatedAgent | protected |
| _myDeathRadius | simulator.agent.LocatedAgent | protected |
| _myDivRadius | simulator.agent.LocatedAgent | protected |
| _myNeighbors | simulator.agent.LocatedAgent | protected |
| _netGrowthRate | simulator.agent.ActiveAgent | protected |
| _netVolumeRate | simulator.agent.ActiveAgent | protected |
| _newLoc | simulator.agent.LocatedAgent | protectedstatic |
| _radius | simulator.agent.LocatedAgent | protected |
| _species | simulator.agent.SpecialisedAgent | protected |
| _speciesParam | simulator.agent.SpecialisedAgent | protected |
| _timeSinceLastDivisionCheck | simulator.agent.LocatedAgent | |
| _totalMass | simulator.agent.ActiveAgent | protected |
| _totalRadius | simulator.agent.LocatedAgent | protected |
| _totalVolume | simulator.agent.LocatedAgent | protected |
| _volume | simulator.agent.LocatedAgent | protected |
| ActiveAgent() | simulator.agent.ActiveAgent | |
| addActiveReaction(Reaction aReaction, boolean useDefaultParam) | simulator.agent.ActiveAgent | |
| addMovement(ContinuousVector aMove) | simulator.agent.LocatedAgent | |
| addPushMovement(LocatedAgent aNeighbour, boolean isMutual, double gain) | simulator.agent.LocatedAgent | |
| addReaction(Reaction aReaction, boolean useDefaultParam) | simulator.agent.ActiveAgent | |
| addSpringMovement(LocatedAgent aNeighbor, boolean isMutual, double gain) | simulator.agent.LocatedAgent | |
| Agent() | simulator.agent.Agent | |
| allReactions | simulator.agent.ActiveAgent | |
| BactAdaptable() | simulator.agent.zoo.BactAdaptable | |
| BactEPS() | simulator.agent.zoo.BactEPS | |
| Bacterium() | simulator.agent.zoo.Bacterium | |
| checkBoundaries() | simulator.agent.LocatedAgent | |
| clone() | simulator.agent.zoo.Bacterium | |
| computeDifferenceVector(ContinuousVector me, ContinuousVector him) | simulator.agent.LocatedAgent | |
| createNewAgent(ContinuousVector position) | simulator.agent.zoo.Bacterium | |
| simulator::agent::ActiveAgent.createNewAgent() | simulator.agent.ActiveAgent | virtual |
| death | simulator.agent.SpecialisedAgent | |
| detPriority | simulator.agent.LocatedAgent | |
| die(boolean isStarving) | simulator.agent.zoo.Bacterium | |
| divide() | simulator.agent.LocatedAgent | |
| divideCompounds(LocatedAgent baby, double babyMassFrac) | simulator.agent.LocatedAgent | |
| excreteEPS(double ratio) | simulator.agent.zoo.Bacterium | |
| findCloseSiblings(int indexSpecies) | simulator.agent.LocatedAgent | |
| fitMassOnGrid(SpatialGrid aSpG, int catalystIndex) | simulator.agent.LocatedAgent | |
| fitMassOnGrid(SpatialGrid aSpG) | simulator.agent.LocatedAgent | |
| fitReacRateOnGrid(SpatialGrid aRateGrid, int reactionIndex) | simulator.agent.LocatedAgent | |
| fitVolRateOnGrid(SpatialGrid aSpG) | simulator.agent.LocatedAgent | |
| getActiveFrac() | simulator.agent.zoo.Bacterium | |
| getBabyMassFrac() | simulator.agent.LocatedAgent | |
| getBirthday() | simulator.agent.zoo.Bacterium | |
| getColor() | simulator.agent.zoo.BactAdaptable | |
| getColorCapsule() | simulator.agent.zoo.Bacterium | |
| getDeathRadius() | simulator.agent.LocatedAgent | |
| getDistance(LocatedAgent aLoc) | simulator.agent.LocatedAgent | |
| getDivRadius() | simulator.agent.LocatedAgent | |
| getDomain() | simulator.agent.LocatedAgent | |
| getGridElement() | simulator.agent.LocatedAgent | |
| getGridIndex() | simulator.agent.LocatedAgent | |
| getInteractDistance() | simulator.agent.LocatedAgent | |
| getInteractDistance(LocatedAgent baby) | simulator.agent.LocatedAgent | |
| getLocation() | simulator.agent.LocatedAgent | |
| getMass(boolean withCapsule) | simulator.agent.LocatedAgent | |
| getMaximumRadius() | simulator.agent.LocatedAgent | |
| getMovement() | simulator.agent.LocatedAgent | |
| getName() | simulator.agent.zoo.BactAdaptable | |
| getNetGrowth() | simulator.agent.ActiveAgent | |
| getParticleMass(int particleIndex) | simulator.agent.ActiveAgent | |
| getPotentialShovers(double radius) | simulator.agent.LocatedAgent | |
| getRadius(boolean withCapsule) | simulator.agent.LocatedAgent | |
| getReactionKinetic(int indexReaction) | simulator.agent.ActiveAgent | |
| getShoveFactor() | simulator.agent.LocatedAgent | |
| getShoveRadius() | simulator.agent.LocatedAgent | |
| getSoluteYield(int indexReaction) | simulator.agent.ActiveAgent | |
| getSpecies() | simulator.agent.SpecialisedAgent | |
| getSpeciesParam() | simulator.agent.zoo.BactAdaptable | |
| getTotalMass() | simulator.agent.ActiveAgent | |
| getVolGrowth() | simulator.agent.ActiveAgent | |
| getVolume(boolean withCapsule) | simulator.agent.LocatedAgent | |
| giveName() | simulator.agent.Agent | |
| grow() | simulator.agent.ActiveAgent | protected |
| growthRate | simulator.agent.ActiveAgent | protected |
| guessMass() | simulator.agent.zoo.Bacterium | |
| hasEPS() | simulator.agent.zoo.Bacterium | |
| hasInert() | simulator.agent.zoo.Bacterium | |
| init() | simulator.agent.zoo.Bacterium | |
| initFromProtocolFile(Simulator aSim, XMLParser aSpeciesRoot) | simulator.agent.zoo.BactAdaptable | |
| initFromResultFile(Simulator aSim, String[] singleAgentData) | simulator.agent.zoo.BactAdaptable | |
| interact(boolean MUTUAL, boolean shoveOnly, boolean seq, double gain) | simulator.agent.LocatedAgent | |
| internalStep() | simulator.agent.zoo.BactAdaptable | protectedvirtual |
| isAttached() | simulator.agent.LocatedAgent | |
| isDead | simulator.agent.SpecialisedAgent | |
| isMoving() | simulator.agent.LocatedAgent | |
| LocatedAgent() | simulator.agent.LocatedAgent | |
| makeKid() | simulator.agent.zoo.Bacterium | |
| manageEPS() | simulator.agent.zoo.BactEPS | |
| move() | simulator.agent.LocatedAgent | |
| mutateAgent() | simulator.agent.zoo.Bacterium | |
| mutatePop() | simulator.agent.zoo.Bacterium | |
| nextFamily | simulator.agent.Agent | protectedstatic |
| particleMass | simulator.agent.ActiveAgent | |
| particleYield | simulator.agent.ActiveAgent | |
| pickNeighbor() | simulator.agent.LocatedAgent | |
| reactionActive | simulator.agent.ActiveAgent | protected |
| reactionKinetic | simulator.agent.ActiveAgent | |
| reactionKnown | simulator.agent.ActiveAgent | protected |
| readyToSwitch() | simulator.agent.zoo.BactAdaptable | |
| recordGenealogy(Agent baby) | simulator.agent.Agent | protected |
| registerBirth() | simulator.agent.LocatedAgent | virtual |
| registerOnAllActiveReaction() | simulator.agent.ActiveAgent | |
| removeReaction(Reaction aPathway) | simulator.agent.ActiveAgent | |
| respondToConditions() | simulator.agent.zoo.BactAdaptable | |
| sendHeader() | simulator.agent.zoo.BactAdaptable | |
| sendName() | simulator.agent.Agent | |
| sendNewAgent() | simulator.agent.zoo.Bacterium | virtual |
| setDivisionDirection(double distance) | simulator.agent.LocatedAgent | |
| setGridIndex(int aGridIndex) | simulator.agent.LocatedAgent | |
| setLocation(ContinuousVector cc) | simulator.agent.LocatedAgent | |
| setNetGrowth(double value) | simulator.agent.ActiveAgent | |
| setSpecies(Species aSpecies) | simulator.agent.SpecialisedAgent | |
| setSpeciesParam(SpeciesParam aSpeciesParam) | simulator.agent.SpecialisedAgent | |
| setSwitchState(Boolean newState) | simulator.agent.zoo.BactAdaptable | |
| setSwitchToOff() | simulator.agent.zoo.BactAdaptable | |
| setSwitchToOn() | simulator.agent.zoo.BactAdaptable | |
| soluteYield | simulator.agent.ActiveAgent | |
| SpecialisedAgent() | simulator.agent.SpecialisedAgent | |
| speciesIndex | simulator.agent.SpecialisedAgent | |
| step() | simulator.agent.Agent | |
| switchIsOn() | simulator.agent.zoo.BactAdaptable | |
| switchOffreaction(Reaction aPathway) | simulator.agent.ActiveAgent | |
| switchOnReaction(Reaction aReaction) | simulator.agent.ActiveAgent | |
| switchState | simulator.agent.zoo.BactAdaptable | protected |
| timeOfRequestToSwitchOff | simulator.agent.zoo.BactAdaptable | protected |
| timeOfRequestToSwitchOn | simulator.agent.zoo.BactAdaptable | protected |
| transferCompounds(LocatedAgent baby, double splitRatio) | simulator.agent.LocatedAgent | |
| turnSwitchOff | simulator.agent.zoo.BactAdaptable | protected |
| turnSwitchOn | simulator.agent.zoo.BactAdaptable | protected |
| unregisterFromAllActiveReactions() | simulator.agent.ActiveAgent | |
| updateActiveReactions() | simulator.agent.zoo.BactAdaptable | |
| updateAttachment() | simulator.agent.LocatedAgent | |
| updateMass() | simulator.agent.ActiveAgent | |
| updateRadius() | simulator.agent.LocatedAgent | |
| updateSize() | simulator.agent.LocatedAgent | |
| updateVolume() | simulator.agent.zoo.Bacterium | |
| willDetach() | simulator.agent.SpecialisedAgent | |
| willDie() | simulator.agent.zoo.Bacterium | |
| willDivide() | simulator.agent.LocatedAgent | |
| writeOutput() | simulator.agent.zoo.BactAdaptable | |
| writePOVColorDefinition(FileWriter fr) | simulator.agent.zoo.BactAdaptable | |
1.8.3.1
