org.primordion.cellontro.app
Class XhCell

java.lang.Object
  org.primordion.xholon.base.Xholon
      org.primordion.xholon.base.XholonWithPorts
          org.primordion.cellontro.app.XhCell

All Implemented Interfaces:

IBioXholon, IXholon

public class XhCell

extends XholonWithPorts

implements IBioXholon

An instance of XhCell 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.

TODO Align this application with XhAbstractSbml, and with Xh apps generated from external SBML.

TODO Allow the kinetics to be readily exportable in SBML format.

Since:

0.1 (Created on July 8, 2005)

Author:

Ken Webb

Field Summary

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
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

XhCell()
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	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	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() Search for instances of Xholon with ports that reference this instance.

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, configure, 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, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postOrderPrint, postReconfigure, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, 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, configure, 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, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postConfigure, postOrderPrint, postReconfigure, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, 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_EXT1

public static final int P_SM_EXT1

See Also:

Constant Field Values

P_SM_EXT2

public static final int P_SM_EXT2

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Constant Field Values

P_SM_EXT3

public static final int P_SM_EXT3

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Constant Field Values

P_SM_EXT4

public static final int P_SM_EXT4

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Constant Field Values

P_SM_INT1

public static final int P_SM_INT1

See Also:

Constant Field Values

P_SM_INT2

public static final int P_SM_INT2

See Also:

Constant Field Values

P_SM_INT3

public static final int P_SM_INT3

See Also:

Constant Field Values

P_SM_INT4

public static final int P_SM_INT4

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Constant Field Values

P_SM_SUB1

public static final int P_SM_SUB1

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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_COE1

public static final int P_SM_COE1

See Also:

Constant Field Values

P_SM_PRD1

public static final int P_SM_PRD1

See Also:

Constant Field Values

P_SM_PRD2

public static final int P_SM_PRD2

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P_SM_COE2

public static final int P_SM_COE2

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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

state

public int state

roleName

public java.lang.String roleName

pheneVal

public double pheneVal

securityException

public java.lang.SecurityException securityException

Constructor Detail

XhCell

public XhCell()

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

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

toString

public java.lang.String toString()

Search for instances of Xholon with ports that reference this instance.

Overrides:

toString in class Xholon