org.primordion.cellontro.app
Class XhLife
java.lang.Object
org.primordion.xholon.base.Xholon
org.primordion.xholon.base.XholonWithPorts
org.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):
- If its xhType = XhtypePureActiveObject Then
- It will have a gene value (geneVal) that it gets from its BioXholonClass.
- It will search for adjacent internal (P_SM_INT) and/or external (P_SM_EXT) spaces that
contain phene values, using instructions from BioXholonClass.
- Else if its xhType = xhTypePurePassiveObject Then
- It will have a phene value (pheneVal) that it gets from its BioXholonClass.
- It will probably be acted upon by one or more xhtypePureActiveObject instances
at each time step.
- Else if its xhType = xhtypePureContainer Then
- It is only a container for objects of the other two xhTypes.
- Endif
At act() time (Basic Cell Model):
- If its xhType = XhtypePureActiveObject Then
- If it's an Enzyme Then
- Increment or decrement the internal (P_SM_INT) pheneVal it points to,
by an amount specified by its geneVal.
- Else if it's a Bilayer or a TransportProtein Then
- Move geneVal number of units between the internal (P_SM_INT) pheneVal it points to,
and the external (P_SM_EXT) pheneVal it points to.
- Endif
- Else if its xhType = xhTypePurePassiveObject Then
- Print the current value of its pheneVal.
- Endif
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
| 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.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 |
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
- See Also:
- Constant Field Values
P_SM_EXT2
public static final int P_SM_EXT2
- See Also:
- Constant Field Values
P_SM_INT3
public static final int P_SM_INT3
- See Also:
- Constant Field Values
P_SM_EXT3
public static final int P_SM_EXT3
- See Also:
- Constant Field Values
P_SM_INT4
public static final int P_SM_INT4
- See Also:
- Constant Field Values
P_SM_EXT4
public static final int P_SM_EXT4
- See Also:
- Constant Field Values
P_SM_SUB1
public static final int P_SM_SUB1
- See Also:
- Constant Field Values
P_SM_PRD1
public static final int P_SM_PRD1
- See Also:
- Constant Field Values
P_SM_SUB2
public static final int P_SM_SUB2
- See Also:
- Constant Field Values
P_SM_PRD2
public static final int P_SM_PRD2
- See Also:
- Constant Field Values
P_SM_ACT1
public static final int P_SM_ACT1
- See Also:
- Constant Field Values
P_SM_INH1
public static final int P_SM_INH1
- See Also:
- 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
- See Also:
- 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
- See Also:
- Constant Field Values
P_NUTRIENTS
public static final int P_NUTRIENTS
- See Also:
- Constant Field Values
P_NEURON_IN_SPACE_PASSAGEWAY
public static final int P_NEURON_IN_SPACE_PASSAGEWAY
- See Also:
- Constant Field Values
P_NEURON_OUT_SPACE_PASSAGEWAY
public static final int P_NEURON_OUT_SPACE_PASSAGEWAY
- See Also:
- Constant Field Values
P_MEMBRANE_POTENTIAL
public static final int P_MEMBRANE_POTENTIAL
- See Also:
- Constant Field Values
P_FUSE
public static final int P_FUSE
- See Also:
- Constant Field Values
P_SYN_CLEFT
public static final int P_SYN_CLEFT
- See Also:
- Constant Field Values
P_MOUTH
public static final int P_MOUTH
- See Also:
- Constant Field Values
P_EAT
public static final int P_EAT
- See Also:
- Constant Field Values
P_GUT
public static final int P_GUT
- See Also:
- Constant Field Values
P_DIGESTION
public static final int P_DIGESTION
- See Also:
- Constant Field Values
P_FOOD
public static final int P_FOOD
- See Also:
- Constant Field Values
P_DIGESTED_FOOD
public static final int P_DIGESTED_FOOD
- See Also:
- Constant Field Values
P_COMPLETELY_DIGESTED_FOOD
public static final int P_COMPLETELY_DIGESTED_FOOD
- See Also:
- Constant Field Values
P_ORGANIC_MATTER
public static final int P_ORGANIC_MATTER
- See Also:
- Constant Field Values
P_LEFT_VENTRICLE
public static final int P_LEFT_VENTRICLE
- See Also:
- Constant Field Values
P_BEAT_LEFT_VENTRICLE
public static final int P_BEAT_LEFT_VENTRICLE
- See Also:
- Constant Field Values
P_BEAT_RIGHT_VENTRICLE
public static final int P_BEAT_RIGHT_VENTRICLE
- See Also:
- Constant Field Values
P_BLOOD_FLOW_1
public static final int P_BLOOD_FLOW_1
- See Also:
- Constant Field Values
P_BLOOD_FLOW_2
public static final int P_BLOOD_FLOW_2
- See Also:
- Constant Field Values
P_BLOOD_FLOW_3
public static final int P_BLOOD_FLOW_3
- See Also:
- Constant Field Values
P_BLOOD_FLOW
public static final int P_BLOOD_FLOW
- See Also:
- 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
- See Also:
- Constant Field Values
SOUT_PHOTON
public static final int SOUT_PHOTON
- See Also:
- Constant Field Values
SOUT_POST_SYNAPTIC_POTENTIAL
public static final int SOUT_POST_SYNAPTIC_POTENTIAL
- See Also:
- Constant Field Values
SOUT_ACTION_POTENTIAL
public static final int SOUT_ACTION_POTENTIAL
- See Also:
- Constant Field Values
SOUT_DO_EXOCYTOSIS
public static final int SOUT_DO_EXOCYTOSIS
- See Also:
- Constant Field Values
SOUT_CHEW
public static final int SOUT_CHEW
- See Also:
- Constant Field Values
SOUT_DIGEST
public static final int SOUT_DIGEST
- See Also:
- Constant Field Values
SOUT_TICK
public static final int SOUT_TICK
- See Also:
- Constant Field Values
SOUT_BLOOD_PLASMA
public static final int SOUT_BLOOD_PLASMA
- See Also:
- Constant Field Values
THRESHOLD_POTENTIAL
public static final int THRESHOLD_POTENTIAL
- See Also:
- Constant Field Values
RESTING_POTENTIAL
public static final int RESTING_POTENTIAL
- See Also:
- Constant Field Values
NUM_BP_PER_BV
public static final int NUM_BP_PER_BV
- See Also:
- Constant Field Values
pheneVal
public double pheneVal
Substrate
public static final int Substrate
- See Also:
- Constant Field Values
Product
public static final int Product
- See Also:
- Constant Field Values
Regulation
public static final int Regulation
- See Also:
- Constant Field Values
S_ACTIVATE
public static final int S_ACTIVATE
- See Also:
- Constant Field Values
S_DEACTIVATE
public static final int S_DEACTIVATE
- See Also:
- Constant Field Values
securityException
public java.lang.SecurityException securityException
XhLife
public XhLife()
- Constructor.
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