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java.lang.Object org.primordion.xholon.base.Xholon org.primordion.xholon.base.XholonWithPorts org.primordion.cellontro.app.XhCellAutop
An instance of XhCellAutop 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.
Field Summary | |
static int |
KInVicinity
|
static int |
KLipidDecay
|
static int |
KWaterPressure
|
static int |
MinWater
|
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_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_INT5
|
static int |
P_SM_PRD1
|
static int |
P_SM_PRD2
|
static int |
P_SM_STR3
|
static int |
P_SM_STR4
|
static int |
P_SM_STR5
|
static int |
P_SM_SUB1
|
static int |
P_SM_SUB2
|
double |
pheneVal
|
java.lang.String |
roleName
|
java.lang.SecurityException |
securityException
|
int |
state
|
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 |
Constructor Summary | |
XhCellAutop()
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. |
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 |
preAct()
Do any setup required before doing the main action during a time step. |
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 java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
public static final int P_SM_INT1
public static final int P_SM_EXT1
public static final int P_SM_INT2
public static final int P_SM_EXT2
public static final int P_SM_STR3
public static final int P_SM_INT3
public static final int P_SM_INT4
public static final int P_SM_STR4
public static final int P_SM_INT5
public static final int P_SM_STR5
public static final int P_SM_SUB1
public static final int P_SM_PRD1
public static final int P_SM_SUB2
public static final int P_SM_PRD2
public static final int P_SM_ACT1
public static final int P_SM_INH1
public static final int P_SM_COE1
public static final int P_SM_COE2
public int state
public java.lang.String roleName
public double pheneVal
public static final int KLipidDecay
public static final int KWaterPressure
public static final int KInVicinity
public static final int MinWater
public java.lang.SecurityException securityException
Constructor Detail |
public XhCellAutop()
Method Detail |
public void initialize()
IXholon
initialize
in interface IXholon
initialize
in class XholonWithPorts
public double getVal()
IXholon
getVal
in interface IXholon
getVal
in class Xholon
public double getPheneVal()
IBioXholon
getPheneVal
in interface IBioXholon
public void incPheneVal(double incAmount)
IBioXholon
incPheneVal
in interface IBioXholon
incAmount
- The amount by which to increment the phenotype value.public void decPheneVal(double decAmount)
IBioXholon
decPheneVal
in interface IBioXholon
decAmount
- The amount by which to decrement the phenotype value.public int getNumReactants()
IBioXholon
getNumReactants
in interface IBioXholon
public void setNumReactants(int numR)
IBioXholon
setNumReactants
in interface IBioXholon
numR
- Maximum number of reactants.public int getNumProducts()
IBioXholon
getNumProducts
in interface IBioXholon
public void setNumProducts(int numP)
IBioXholon
setNumProducts
in interface IBioXholon
numP
- Maximum number of products.public int getNumModifiers()
IBioXholon
getNumModifiers
in interface IBioXholon
public void setNumModifiers(int numM)
IBioXholon
setNumModifiers
in interface IBioXholon
numM
- Maximum number of modifiers.public void setRoleName(java.lang.String roleName)
IXholon
setRoleName
in interface IXholon
setRoleName
in class Xholon
public java.lang.String getRoleName()
IXholon
getRoleName
in interface IXholon
getRoleName
in class Xholon
public void configure()
IXholon
configure
in interface IXholon
configure
in class XholonWithPorts
public void preAct()
IXholon
preAct
in interface IXholon
preAct
in class Xholon
public void act()
IXholon
act
in interface IXholon
act
in class Xholon
public java.lang.String toString()
toString
in class Xholon
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