org.primordion.cellontro.app
Class XhAbstractSbml

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

All Implemented Interfaces:

IBioXholon, IXholon

Direct Known Subclasses:

XhBrusselator, XhCellModel, XhCircadianClock, XhDimericMWCstiff, XhGlycolysis, XhGlycolysis_Test, XhGlycolysisTESTXML, XhGlycolysisTESTXML2, XhGlyHunThouBilayer, XhGlyHunThouInhibit, XhGlyMillion, XhGlyTenThou, XhYeastGlyPritchardKel

public abstract class XhAbstractSbml

extends XholonWithPorts

implements IBioXholon

SBML Application.

This class will be automatically extended if you use Sbml2Cellontro to build a Cellontro application that executes a model read from a Systems Biology Markup Language (SBML) file. SBML is used to exchange models between different software packages.

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

Since:

0.2 (Created on December 8, 2005)

Author:

Ken Webb

Field Summary

double	pheneVal
java.lang.String	roleName
java.lang.SecurityException	securityException

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

XhAbstractSbml()
Constructor.

Method Summary

void	configure() Perform some action, typically once at start up; MAY be overridden.
void	decPheneVal(double decAmount) Decrement the phene value by incAmount.
abstract int	getNumModifiers() Get maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.
abstract int	getNumProducts() Get maximum number of products that any xholon instance may have in this model.
abstract 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.
int	getTimeStepMultiplier() Get the time step multiplier, needed for numerical integration.
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.
abstract void	setNumModifiers(int numM) Set maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.
abstract void	setNumProducts(int numP) Set maximum number of products that any xholon instance may have in this model.
abstract 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.
static void	setTimeStepMultiplier(int timeStepMultiplier) Set the time step multiplier, needed for numerical integration.
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

act, 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, postAct, 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

act, 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, postAct, 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

roleName

public java.lang.String roleName

pheneVal

public double pheneVal

securityException

public java.lang.SecurityException securityException

Constructor Detail

XhAbstractSbml

public XhAbstractSbml()

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.

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

getNumReactants

public abstract 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 abstract 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 abstract 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 abstract 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 abstract 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 abstract 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.

getTimeStepMultiplier

public int getTimeStepMultiplier()

Get the time step multiplier, needed for numerical integration.

Returns:

Time step multiplier.

setTimeStepMultiplier

public static void setTimeStepMultiplier(int timeStepMultiplier)

Set the time step multiplier, needed for numerical integration.

Parameters:

timeStepMultiplier - Time step multiplier.

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

toString

public java.lang.String toString()

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

Overrides:

toString in class Xholon