org.primordion.cellontro.app
Class XhLife

java.lang.Object
  extended byorg.primordion.xholon.base.Xholon
      extended byorg.primordion.xholon.base.XholonWithPorts
          extended byorg.primordion.cellontro.app.XhLife
All Implemented Interfaces:
CeLife, IBioXholon, IXholon

public class XhLife
extends XholonWithPorts
implements IBioXholon, CeLife

An instance of XhLife represents some biological entity, and exists as a node in a composite structure hierarchy tree. Each such Xholon object goes through an initial configure() process, and may subsequently go through a regular act() process at each time step.

At configure() time (Basic Cell Model):

At act() time (Basic Cell Model):

An enzyme active object is a simple abstraction of a biological enzyme that acts on small molecules contained within the same internal space. A bilayer is a simple abstraction of a biological membrane (lipid bilayer) that moves small molecules between its internal space and the space external to it. A transport protein is a simple abstraction that acts much like a bilayer.

Since:
0.1 (Created on July 8, 2005)
Author:
Ken Webb

Field Summary
static int ARROW_OF_TIME_FREQ
           
static int NUM_BP_PER_BV
           
static int P_BEAT_LEFT_VENTRICLE
           
static int P_BEAT_RIGHT_VENTRICLE
           
static int P_BLOOD_FLOW
           
static int P_BLOOD_FLOW_1
           
static int P_BLOOD_FLOW_2
           
static int P_BLOOD_FLOW_3
           
static int P_CALCIUM
           
static int P_COMPLETELY_DIGESTED_FOOD
           
static int P_DIGESTED_FOOD
           
static int P_DIGESTION
           
static int P_EAT
           
static int P_FOOD
           
static int P_FUSE
           
static int P_GUT
           
static int P_LEFT_VENTRICLE
           
static int P_MEMBRANE_POTENTIAL
           
static int P_MOUTH
           
static int P_NEURON_IN_SPACE_PASSAGEWAY
           
static int P_NEURON_OUT_SPACE_PASSAGEWAY
           
static int P_NUTRIENTS
           
static int P_ORGANIC_MATTER
           
static int P_REFLECTED_LIGHT
           
static int P_SM_ACT1
           
static int P_SM_COE1
           
static int P_SM_COE2
           
static int P_SM_EXT1
           
static int P_SM_EXT2
           
static int P_SM_EXT3
           
static int P_SM_EXT4
           
static int P_SM_INH1
           
static int P_SM_INT1
           
static int P_SM_INT2
           
static int P_SM_INT3
           
static int P_SM_INT4
           
static int P_SM_PRD1
           
static int P_SM_PRD2
           
static int P_SM_SUB1
           
static int P_SM_SUB2
           
static int P_SOLAR_ENERGY
           
static int P_SYN_CLEFT
           
 double pheneVal
           
static int Product
           
static int Regulation
           
static int RESTING_POTENTIAL
           
 java.lang.String roleName
           
static int S_ACTIVATE
           
static int S_DEACTIVATE
           
 java.lang.SecurityException securityException
           
static int SOUT_ACTION_POTENTIAL
           
static int SOUT_BLOOD_PLASMA
           
static int SOUT_CHEW
           
static int SOUT_DIGEST
           
static int SOUT_DO_EXOCYTOSIS
           
static int SOUT_PHOTON
           
static int SOUT_POST_SYNAPTIC_POTENTIAL
           
static int SOUT_TICK
           
 int state
           
static int Substrate
           
static int THRESHOLD_POTENTIAL
           
 
Fields inherited from class org.primordion.xholon.base.XholonWithPorts
port
 
Fields inherited from class org.primordion.xholon.base.Xholon
DEFAULT_LEVEL, interaction, interactionsEnabled
 
Fields inherited from interface org.primordion.xholon.base.IXholon
DEFAULT_SIZE_MSG_Q, NINCLUDE_PSC, NINCLUDE_PSx, NINCLUDE_PxC, NINCLUDE_Pxx, NINCLUDE_xSC, NINCLUDE_xSx, NINCLUDE_xxC, NINCLUDE_xxx
 
Fields inherited from interface org.primordion.cellontro.app.CeLife
A_KetoglutarateCE, A_KetoglutarateDehydrogenaseCE, ACarbonCE, AcetateCE, AcetylcholinesteraseCE, AcetylCoACE, AconitaseCE, AdenineCE, AfferentCentralNeuronCE, AlaCE, AlcoholDehydrogenaseCE, AldolaseCE, AminoAcidCE, AminoAcidPaletteCE, AminoGroupCE, AmpaKainateReceptorCE, AmpCE, AnchorProteinCE, AndrogenCE, AnimalCE, ArchebacteriaCE, ArgCE, ArteryCE, AsnCE, AspCE, AstrocyteCE, AstrocyteCellBodyCE, AstrocyteFootCapillaryCE, AstrocyteFootCE, AstrocyteFootNeuronCE, AstrocyteWithInnardsCE, AtmosphereCE, AtriumCE, AttributeCE, AxonBilayerCE, AxonCE, AxonHillockCE, AxonMembraneCE, AxonSegmentCE, AxonSegmentSplitterCE, BaseCE, BaseSugarCE, BipolarCellCE, BloodPlasmaCE, BloodVesselCE, BodyOfWaterCE, BoneMarrowCE, BovineRibonucleaseCE, BovineRibonucleaseMoleculeCE, BovineRibonucleasePPCE, BovineRibonucleaseWithAaActorsCE, BrainCE, CaCE, CapillaryCE, CarbonDioxideCE, CarboxylGroupCE, CelestialBodyCE, CeliacGanglionCE, CellBilayerCE, CellMembraneCE, CellularSolutionCE, CellularSpaceCE, CellWallCE, CentralNervousSystemCE, CentralNeuronCE, CerebellumCE, CerebralCortexCE, CerebrumCE, ChloroplastBilayerCE, ChloroplastCE, ChloroplastDualMembraneCE, ChloroplastFluidCE, ChloroplastIntermembraneSpaceCE, ChloroplastMembraneCE, CholesterolCE, CholineCE, ChromosomeCE, CirculatorySystemCE, CisternaeCE, CisternalSpaceCE, CitrateCE, CitrateSynthaseCE, CmpCE, ColonCE, ConeCE, ConeOuterSegmentCE, ConfigurationAgentCE, CtfCE, CysCE, CytoplasmCE, CytosineCE, CytoSkeletonCE, CytosolCE, DAmpCE, DCmpCE, DendriteBilayerCE, DendriteCE, DendriteMembraneCE, DendritesCE, DeoxyriboseCE, DGmpCE, DiencephalonCE, DigestedFoodCE, DigestiveSystemCE, DihydroxyacetonePhosphateCE, DnaCE, DnaNucleotideCE, DnaTest1CE, DorsalHornLeftCE, DorsalHornRightCE, DorsalRootGanglionCE, DTmpCE, EarthCE, EfferentCentralNeuronCE, EnclosedSpaceCE, EndoplasmicReticulumCE, EndosomeBilayerCE, EndosomeCE, EndosomeFluidCE, EndosomeMembraneCE, EndosomeSpaceCE, EnolaseCE, EnzymeCE, ErBilayerCE, ErFluidCE, ErMembraneCE, ErythrocyteCE, EsophagusCE, EstradiolCE, EstrogenCE, EthanolamineCE, EubacteriaCE, EukaryoteCE, EukaryoticCellCE, ExtraCellularSolutionCE, ExtraCellularSpaceCE, EyeCE, FibrilCE, FilamentCE, FoodCE, ForeBrainCE, FreeNerveEndingCE, FreeNerveEndingNeuronCE, Fructose_1x6_BiphosphateCE, Fructose_1x6_bisphosphataseCE, Fructose_2x6_BiphosphateCE, Fructose_6_PhosphateCE, FumarateCE, FumarateHydrataseCE, GabaAReceptorCE, GaiaCE, Galactose_1_PhosphateCE, GanglionCellCE, GaseousSolutionCE, GlnCE, GlucagonCE, GluCE, Glucose_1_PhosphateCE, Glucose_6_phosphataseCE, Glucose_6_PhosphateCE, GlucoseCE, GlutamateCE, GlyCE, Glyceraldehyde_3_PhosphateCE, Glyceraldehyde_3_phosphateDehydrogenaseCE, GlycerolCE, GlycerolPhosphateCE, GlycogenCE, GlycolipidCE, GlycolysisEnzymeCE, GmpCE, GolgiBilayerCE, GolgiComplexCE, GolgiFluidCE, GolgiMembraneCE, GolgiSacculeCE, GolgiSpaceCE, GPaseCE, GPaseSystemCE, GranuleCE, GranumCE, GuanineCE, HCE, HeartCE, HeatCE, HemeCE, HemoglobinCE, HemoglobinMoleculeCE, HemoglobinPPaCE, HemoglobinPPbCE, HexokinaseCE, HindBrainCE, HisCE, HumanBeingCE, HydrogenAtomCE, HypoThalamusCE, IleCE, includeCE, InferiorMesentericGanglionCE, InorganicPrecursorCE, IntermediateFilamentCE, InternalSpaceCE, InterNeuronCE, IonCE, IsocitrateCE, IsocitrateDehydrogenaseCE, KCE, LactateDehydrogenaseCE, LandCE, LargeIntestineCE, LateralGeniculateNucleusCE, LeftAtriumCE, LeftVentricleCE, LettuceCE, LeuCE, LgNeuroreceptorCE, LifeTheUniverseAndEverythingCE, LipidBilayerCE, LipidCE, LipidDisintegrationCE, LipidLayerCE, LipidNonPolarTailCE, LipidPolarHeadCE, LungCE, LysCE, LysosomeBilayerCE, LysosomeCE, LysosomeFluidCE, LysosomeMembraneCE, LysosomeSpaceCE, MalateCE, MalateDehydrogenaseCE, Mannose_6_PhosphateCE, MatrixCE, MatrixsolCE, MechanoReceptorCE, MechanoReceptorNeuronCE, MedullaCE, MeissnerCorpuscleCE, MeissnerCorpuscleNeuronCE, MembraneCE, MembranePotentialCE, MerkelsDiskCE, MerkelsDiskNeuronCE, MetCE, MicroFilamentCE, MicroTubuleCE, MidBrainCE, MitochondrialDualMembraneCE, MitochondrialInnerBilayerCE, MitochondrialInnerMembraneCE, MitochondrialIntermembranesolCE, MitochondrialIntermembraneSpaceCE, MitochondrialOuterBilayerCE, MitochondrialOuterMembraneCE, MitochondrionCE, MotorCortexCE, MotorEndPlateCE, MotorNeuronCE, MouthCE, MRnaCE, MRnaTest1CE, MucosalCellCE, MucosalCellMembraneCE, MuscleCE, MuscleCellBodyCE, MuscleFiberCE, MuscleSpindleCE, MuscleSpindleNeuronCE, MyelinCellCE, NaCE, NervousSystemCE, NervousSystemEntityCE, NervousSystemModelCE, NeuronCapillaryConnectorCE, NeuronCapillaryConnectorsCE, NeuronCE, NeuronCellBodyCE, NeuronSystem1CE, NeurotransmitterCE, NicotinicAChReceptorCE, NmdaReceptorCE, NuclearEnvelopeCE, NuclearInnerBilayerCE, NuclearInnerMembraneCE, NuclearLaminaCE, NuclearOuterBilayerCE, NuclearOuterMembraneCE, NuclearPoreAqueousChannelCE, NuclearPoreCE, NucleoidCE, NucleolusCE, NucleoplasmCE, NucleosolCE, NucleotideCE, NucleusCE, OligodendrocyteCE, OrganicMatterCE, OxaloacetateCE, OxygenCE, PacinianCorpuscleCE, PacinianCorpuscleNeuronCE, Page320KinaseCE, Page320PhosphataseCE, PalmitateCE, ParasymOrganGanglionCE, PE_InVicinityCE, PerinuclearFluidCE, PerinuclearSpaceCE, PeripheralNervousSystemCE, PeroxisomeBilayerCE, PeroxisomeCE, PeroxisomeFluidCE, PeroxisomeMembraneCE, PeroxisomeSpaceCE, Pfk_2CE, PheCE, PhosphateGroupCE, Phosphatidic_Acid_PhosphataseCE, Phosphatidic_AcidCE, Phosphatidyl_EthanolamineCE, PhosphoenolPyruvateCarboxykinaseCE, PhosphoEnolPyruvateCE, PhosphoFructokinaseCE, PhosphoGlucoIsomeraseCE, PhosphoGlycerokinaseCE, PhosphoGlyceromutaseCE, PhospholipidCE, PhotoReceptorCE, PhotoReceptorNeuronCE, PKinaseCE, PlantCE, PolyPeptideCE, PolysaccharideCE, PonsCE, PPhosphataseCE, PrimaryVisualCortexCE, PrionCE, ProCE, ProgesteroneCE, ProkaryoteCE, ProkaryoticCellCE, PurineCE, PyrimidineCE, PyruvateCarboxylaseCE, PyruvateCE, PyruvateDecarboxylaseCE, PyruvateDehydrogenaseCE, PyruvateKinaseCE, PyruvateTransporterCE, RcsEnzymeCE, RectumCE, RegulatoryComplexCE, RetinaCE, RetinaConesAndRodsCE, RgAlaCE, RgArgCE, RgAsnCE, RgAspCE, RgCysCE, RgGlnCE, RgGluCE, RgGlyCE, RgHisCE, RgIleCE, RgLeuCE, RgLysCE, RgMetCE, RgPheCE, RgProCE, RGroupCE, RgSerCE, RgThrCE, RgTrpCE, RgTyrCE, RgValCE, RiboseCE, RibosomeCE, RightAtriumCE, RightVentricleCE, RingSubunitCE, RnaNucleotideCE, RnaPolymeraseCE, RnaPolymeraseICE, RnaPolymeraseIICE, RnaPolymeraseIIICE, RockCE, RodCE, RodOuterSegmentCE, RoughErCE, RRnaCE, RuffinisCorpuscleCE, RuffinisCorpuscleNeuronCE, SchwannCellCE, SecretoryVesicleBilayerCE, SecretoryVesicleCE, SecretoryVesicleFluidCE, SecretoryVesicleMembraneCE, SecretoryVesicleSpaceCE, SensorCE, SensoryReceptorNeuronCE, SerCE, SimpleEcologyCE, SingleCellCE, SkeletalMuscleCellCE, SmallIntestineCE, SmallMoleculeCE, SmoothErCE, SoilCE, SolarSystemCE, SolutionCE, SolventCE, Sp1CE, SphingolipidCE, SpinalArteryCE, SpinalCordCE, SpinalCordCervicalRegionCE, SpinalCordCoccygealRegionCE, SpinalCordLumbarRegionCE, SpinalCordRegionCE, SpinalCordSacralRegionCE, SpinalCordThoracicRegionCE, SpinalInterNeuronCE, SpinalVeinCE, SpokeCE, SteroidCE, SteroidHormoneCE, StomachCE, StromaLamellaeCE, StructuredClassifierCE, SuccinateCE, SuccinateDehydrogenaseCE, SuccinylCoaCE, SuccinylCoASynthetaseCE, SucraseCE, SucroseCE, SucroseTransporterCE, SunCE, SympatheticChainCE, SympatheticChainGanglionCE, SynapsesCE, SynapticCleftCE, SynapticCleftFluidCE, SynapticVesicleBilayerCE, SynapticVesicleCE, SynapticVesicleFluidCE, SynapticVesicleMembraneCE, SynapticVesicleSpaceCE, SynaptotagminCE, TcaEnzymeCE, TerminalButtonBilayerCE, TerminalButtonCE, TerminalButtonFluidCE, TerminalButtonMembraneCE, TerminalButtonPlasmCE, TerminalButtonsCE, TestosteroneCE, TfIIBCE, TfIIDCE, TfIIECE, TfIIFCE, TfIIHCE, ThalamusCE, TheArrowOfTimeCE, ThrCE, ThylakoidCE, ThymineCE, TranscriptionComplexCE, TranscriptionComplexICE, TranscriptionComplexIICE, TranscriptionComplexIIICE, TranscriptionFactorBCE, TranscriptionFactorBPassiveCE, TranscriptionFactorRCE, TransporterCE, TransportProteinCE, TriglycerideCE, Triose_P_IsomeraseCE, TriosePhosphateIsomeraseCE, TRnaCE, TrpCE, TyrCE, UDP_GalactoseCE, UDP_GlucoseCE, UmpCE, UracilCE, VacuoleBilayerCE, VacuoleCE, VacuoleMembraneCE, ValCE, variousPhospholipidSubclassesCE, VeinCE, VentralHornLeftCE, VentralHornParasymCE, VentralHornRightCE, VentralHornSymCE, VentricleCE, VesFusionProteinCE, VesicleCE, ViroidCE, VirusCE, VoltageGatedCaChannelCE, VoltageGatedChannelCE, VoltageGatedKChannelCE, VoltageGatedNaChannelCE, WaterCE, X1x3_BisphosphoGlycerateCE, X2_PhosphoGlycerateCE, X3_PhosphoGlycerateCE, XholonClassCE
 
Constructor Summary
XhLife()
          Constructor.
 
Method Summary
 void act()
          Do some action during this time step.
 void configure()
          Perform some action, typically once at start up; MAY be overridden.
 int configure(java.lang.String instructions, int instructIx)
          Configure something based on a configure instruction.
 void decPheneVal(double decAmount)
          Decrement the phene value by incAmount.
 int getNumModifiers()
          Get maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.
 int getNumProducts()
          Get maximum number of products that any xholon instance may have in this model.
 int getNumReactants()
          Get maximum number of reactants (substrates) that any xholon instance may have in this model.
 double getPheneVal()
          Get phene value.
 java.lang.String getRoleName()
          Get name of the role played by this Xholon within a specific context.
 double getVal()
          Get the value of a "double" maintained by this xholon instance.
 void incPheneVal(double incAmount)
          Increment the phene value by incAmount.
 void initialize()
          Initialize the tree node.
 void performActivity(int activityId, IMessage msg)
          Do the UML2 Activity identified by the activityId.
 boolean performGuard(int activityId, IMessage msg)
          Do the UML2 Activity identified by the activityId.
 void postAct()
          Do any required work after doing the main action during a time step.
 void preAct()
          Do any setup required before doing the main action during a time step.
 void processReceivedMessage(Message msg)
          Process a received ROOM/UML2 message taken from the message queue.
 void setNumModifiers(int numM)
          Set maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.
 void setNumProducts(int numP)
          Set maximum number of products that any xholon instance may have in this model.
 void setNumReactants(int numR)
          Set maximum number of reactants (substrates) that any xholon instance may have in this model.
 void setRoleName(java.lang.String roleName)
          Set name of the role played by this Xholon within a specific context.
 java.lang.String toString()
           
 
Methods inherited from class org.primordion.xholon.base.XholonWithPorts
getMaxPorts, getPort, isActiveObject, isBound, isContainer, isPassiveObject, postConfigure, setMaxPorts, setPorts, terminate
 
Methods inherited from class org.primordion.xholon.base.Xholon
appendChild, appendChild, appendChild, cleanup, createStructure, decVal, decVal, depth, draw, getChildNodes, getFirstChild, getFirstSibling, getId, getLastChild, getLastSibling, getName, getNeighbors, getNextId, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumSiblings, getParentNode, getPreviousSibling, getRootNode, getSiblings, getSizeMessageQ, getUid, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getXhc, getXhcId, getXhcName, getXhType, handleNodeSelection, hasAncestor, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, height, incVal, incVal, initStatics, inOrderPrint, insertAfter, insertBefore, insertFirstChild, isExternal, isInternal, isLeaf, isRootNode, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performVoidActivity, postOrderPrint, postReconfigure, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, reconfigure, remove, removeChild, resetNextId, sendMessage, sendMessage, sendMessage, setAttributeVal, setFactory, setFirstChild, setId, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setSizeMessageQ, setUid, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVariableValue, setXhc, swapNode, treeSize, writeXml
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.primordion.xholon.base.IXholon
appendChild, appendChild, appendChild, cleanup, createStructure, decVal, decVal, depth, draw, getChildNodes, getFirstChild, getFirstSibling, getId, getLastChild, getLastSibling, getName, getNeighbors, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumSiblings, getParentNode, getPort, getPreviousSibling, getRootNode, getSiblings, getUid, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getXhc, getXhcId, getXhcName, getXhType, handleNodeSelection, hasAncestor, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, height, incVal, incVal, initStatics, inOrderPrint, insertAfter, insertBefore, insertFirstChild, isActiveObject, isBound, isContainer, isExternal, isInternal, isLeaf, isPassiveObject, isRootNode, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performVoidActivity, postConfigure, postOrderPrint, postReconfigure, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, reconfigure, remove, removeChild, sendMessage, sendMessage, sendMessage, setAttributeVal, setFirstChild, setId, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setPorts, setUid, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVariableValue, setXhc, swapNode, terminate, treeSize, writeXml
 

Field Detail

P_SM_INT1

public static final int P_SM_INT1
See Also:
Constant Field Values

P_SM_EXT1

public static final int P_SM_EXT1
See Also:
Constant Field Values

P_SM_INT2

public static final int P_SM_INT2
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P_SM_EXT2

public static final int P_SM_EXT2
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P_SM_INT3

public static final int P_SM_INT3
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P_SM_EXT3

public static final int P_SM_EXT3
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P_SM_INT4

public static final int P_SM_INT4
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P_SM_EXT4

public static final int P_SM_EXT4
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P_SM_SUB1

public static final int P_SM_SUB1
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Constant Field Values

P_SM_PRD1

public static final int P_SM_PRD1
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Constant Field Values

P_SM_SUB2

public static final int P_SM_SUB2
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Constant Field Values

P_SM_PRD2

public static final int P_SM_PRD2
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Constant Field Values

P_SM_ACT1

public static final int P_SM_ACT1
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Constant Field Values

P_SM_INH1

public static final int P_SM_INH1
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Constant Field Values

P_SM_COE1

public static final int P_SM_COE1
See Also:
Constant Field Values

P_SM_COE2

public static final int P_SM_COE2
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Constant Field Values

P_SOLAR_ENERGY

public static final int P_SOLAR_ENERGY
See Also:
Constant Field Values

P_CALCIUM

public static final int P_CALCIUM
See Also:
Constant Field Values

P_REFLECTED_LIGHT

public static final int P_REFLECTED_LIGHT
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Constant Field Values

P_NUTRIENTS

public static final int P_NUTRIENTS
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Constant Field Values

P_NEURON_IN_SPACE_PASSAGEWAY

public static final int P_NEURON_IN_SPACE_PASSAGEWAY
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Constant Field Values

P_NEURON_OUT_SPACE_PASSAGEWAY

public static final int P_NEURON_OUT_SPACE_PASSAGEWAY
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Constant Field Values

P_MEMBRANE_POTENTIAL

public static final int P_MEMBRANE_POTENTIAL
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Constant Field Values

P_FUSE

public static final int P_FUSE
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Constant Field Values

P_SYN_CLEFT

public static final int P_SYN_CLEFT
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Constant Field Values

P_MOUTH

public static final int P_MOUTH
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Constant Field Values

P_EAT

public static final int P_EAT
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Constant Field Values

P_GUT

public static final int P_GUT
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Constant Field Values

P_DIGESTION

public static final int P_DIGESTION
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Constant Field Values

P_FOOD

public static final int P_FOOD
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Constant Field Values

P_DIGESTED_FOOD

public static final int P_DIGESTED_FOOD
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Constant Field Values

P_COMPLETELY_DIGESTED_FOOD

public static final int P_COMPLETELY_DIGESTED_FOOD
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Constant Field Values

P_ORGANIC_MATTER

public static final int P_ORGANIC_MATTER
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Constant Field Values

P_LEFT_VENTRICLE

public static final int P_LEFT_VENTRICLE
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Constant Field Values

P_BEAT_LEFT_VENTRICLE

public static final int P_BEAT_LEFT_VENTRICLE
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P_BEAT_RIGHT_VENTRICLE

public static final int P_BEAT_RIGHT_VENTRICLE
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Constant Field Values

P_BLOOD_FLOW_1

public static final int P_BLOOD_FLOW_1
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P_BLOOD_FLOW_2

public static final int P_BLOOD_FLOW_2
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P_BLOOD_FLOW_3

public static final int P_BLOOD_FLOW_3
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P_BLOOD_FLOW

public static final int P_BLOOD_FLOW
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Constant Field Values

state

public int state

roleName

public java.lang.String roleName

ARROW_OF_TIME_FREQ

public static final int ARROW_OF_TIME_FREQ
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Constant Field Values

SOUT_PHOTON

public static final int SOUT_PHOTON
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Constant Field Values

SOUT_POST_SYNAPTIC_POTENTIAL

public static final int SOUT_POST_SYNAPTIC_POTENTIAL
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Constant Field Values

SOUT_ACTION_POTENTIAL

public static final int SOUT_ACTION_POTENTIAL
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Constant Field Values

SOUT_DO_EXOCYTOSIS

public static final int SOUT_DO_EXOCYTOSIS
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SOUT_CHEW

public static final int SOUT_CHEW
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SOUT_DIGEST

public static final int SOUT_DIGEST
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SOUT_TICK

public static final int SOUT_TICK
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SOUT_BLOOD_PLASMA

public static final int SOUT_BLOOD_PLASMA
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Constant Field Values

THRESHOLD_POTENTIAL

public static final int THRESHOLD_POTENTIAL
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Constant Field Values

RESTING_POTENTIAL

public static final int RESTING_POTENTIAL
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Constant Field Values

NUM_BP_PER_BV

public static final int NUM_BP_PER_BV
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Constant Field Values

pheneVal

public double pheneVal

Substrate

public static final int Substrate
See Also:
Constant Field Values

Product

public static final int Product
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Regulation

public static final int Regulation
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Constant Field Values

S_ACTIVATE

public static final int S_ACTIVATE
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S_DEACTIVATE

public static final int S_DEACTIVATE
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Constant Field Values

securityException

public java.lang.SecurityException securityException
Constructor Detail

XhLife

public XhLife()
Constructor.

Method Detail

initialize

public void initialize()
Description copied from interface: IXholon
Initialize the tree node. Typically this is only used to re-initialize a node, such as when it is reused through the TreeNodeFactoryStatic.

Specified by:
initialize in interface IXholon
Overrides:
initialize in class XholonWithPorts

getVal

public double getVal()
Description copied from interface: IXholon
Get the value of a "double" maintained by this xholon instance. If a class that implements this interface does not maintain such a value, it should return 0.0 This method can be used in place of getVal_double()

Specified by:
getVal in interface IXholon
Overrides:
getVal in class Xholon

getPheneVal

public double getPheneVal()
Description copied from interface: IBioXholon
Get phene value.

Specified by:
getPheneVal in interface IBioXholon
Returns:
The phenotype value.

incPheneVal

public void incPheneVal(double incAmount)
Description copied from interface: IBioXholon
Increment the phene value by incAmount.

Specified by:
incPheneVal in interface IBioXholon
Parameters:
incAmount - The amount by which to increment the phenotype value.

decPheneVal

public void decPheneVal(double decAmount)
Description copied from interface: IBioXholon
Decrement the phene value by incAmount.

Specified by:
decPheneVal in interface IBioXholon
Parameters:
decAmount - The amount by which to decrement the phenotype value.

getNumReactants

public int getNumReactants()
Description copied from interface: IBioXholon
Get maximum number of reactants (substrates) that any xholon instance may have in this model.

Specified by:
getNumReactants in interface IBioXholon
Returns:
Maximum number of reactants.

setNumReactants

public void setNumReactants(int numR)
Description copied from interface: IBioXholon
Set maximum number of reactants (substrates) that any xholon instance may have in this model.

Specified by:
setNumReactants in interface IBioXholon
Parameters:
numR - Maximum number of reactants.

getNumProducts

public int getNumProducts()
Description copied from interface: IBioXholon
Get maximum number of products that any xholon instance may have in this model.

Specified by:
getNumProducts in interface IBioXholon
Returns:
Maximum number of products.

setNumProducts

public void setNumProducts(int numP)
Description copied from interface: IBioXholon
Set maximum number of products that any xholon instance may have in this model.

Specified by:
setNumProducts in interface IBioXholon
Parameters:
numP - Maximum number of products.

getNumModifiers

public int getNumModifiers()
Description copied from interface: IBioXholon
Get maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.

Specified by:
getNumModifiers in interface IBioXholon
Returns:
Maximum number of modifiers.

setNumModifiers

public void setNumModifiers(int numM)
Description copied from interface: IBioXholon
Set maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.

Specified by:
setNumModifiers in interface IBioXholon
Parameters:
numM - Maximum number of modifiers.

setRoleName

public void setRoleName(java.lang.String roleName)
Description copied from interface: IXholon
Set name of the role played by this Xholon within a specific context.

Specified by:
setRoleName in interface IXholon
Overrides:
setRoleName in class Xholon

getRoleName

public java.lang.String getRoleName()
Description copied from interface: IXholon
Get name of the role played by this Xholon within a specific context.

Specified by:
getRoleName in interface IXholon
Overrides:
getRoleName in class Xholon

configure

public void configure()
Description copied from interface: IXholon
Perform some action, typically once at start up; MAY be overridden. Recursive; application should call this only for root.

Specified by:
configure in interface IXholon
Overrides:
configure in class XholonWithPorts

configure

public int configure(java.lang.String instructions,
                     int instructIx)
Description copied from interface: IXholon
Configure something based on a configure instruction.

Specified by:
configure in interface IXholon
Overrides:
configure in class Xholon

preAct

public void preAct()
Description copied from interface: IXholon
Do any setup required before doing the main action during a time step.

Specified by:
preAct in interface IXholon
Overrides:
preAct in class Xholon

act

public void act()
Description copied from interface: IXholon
Do some action during this time step. Typically all nodes in the tree will do their pre-actions (optional), then all will do their actions, and then all will do their post-actions (optional).

Specified by:
act in interface IXholon
Overrides:
act in class Xholon

postAct

public void postAct()
Description copied from interface: IXholon
Do any required work after doing the main action during a time step.

Specified by:
postAct in interface IXholon
Overrides:
postAct in class Xholon

processReceivedMessage

public void processReceivedMessage(Message msg)
Description copied from interface: IXholon
Process a received ROOM/UML2 message taken from the message queue. All sent messages are placed in queues before they are processed.

Specified by:
processReceivedMessage in interface IXholon
Overrides:
processReceivedMessage in class Xholon

performActivity

public void performActivity(int activityId,
                            IMessage msg)
Description copied from interface: IXholon
Do the UML2 Activity identified by the activityId. This is code called during a state Transition, or while entering, exiting, or within a State.

Specified by:
performActivity in interface IXholon
Overrides:
performActivity in class Xholon

performGuard

public boolean performGuard(int activityId,
                            IMessage msg)
Description copied from interface: IXholon
Do the UML2 Activity identified by the activityId. This is code called before a Transition from a State or Choice, to check the Guard conditions.

Specified by:
performGuard in interface IXholon
Overrides:
performGuard in class Xholon

toString

public java.lang.String toString()
Overrides:
toString in class Xholon