org.primordion.cellontro.base
Interface IBioXholon

All Superinterfaces:

IXholon

All Known Implementing Classes:

XhAbstractSbml, XhCell, XhCellAutop, XhLife

public interface IBioXholon

extends IXholon

An instance of IBioXholon represents some biological entity, and exists as a node in a composite structure hierarchy tree. Each such IXholon 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 12, 2005)

Author:

Ken Webb

Field Summary

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

Method Summary

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.
void	incPheneVal(double incAmount) Increment the phene value by incAmount.
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.

Methods inherited from interface org.primordion.xholon.base.IXholon

act, appendChild, appendChild, appendChild, cleanup, configure, configure, createStructure, decVal, decVal, depth, draw, getChildNodes, getFirstChild, getFirstSibling, getId, getLastChild, getLastSibling, getName, getNeighbors, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumSiblings, getParentNode, getPort, getPreviousSibling, getRoleName, getRootNode, getSiblings, getUid, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getVal, getXhc, getXhcId, getXhcName, getXhType, handleNodeSelection, hasAncestor, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, height, incVal, incVal, initialize, initStatics, inOrderPrint, insertAfter, insertBefore, insertFirstChild, isActiveObject, isBound, isContainer, isExternal, isInternal, isLeaf, isPassiveObject, isRootNode, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postConfigure, postOrderPrint, postReconfigure, preAct, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, reconfigure, remove, removeChild, sendMessage, sendMessage, sendMessage, setAttributeVal, setFirstChild, setId, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setPorts, setRoleName, setUid, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVariableValue, setXhc, swapNode, terminate, treeSize, writeXml

Method Detail

getPheneVal

public double getPheneVal()

Get phene value.

Returns:

The phenotype value.

incPheneVal

public void incPheneVal(double incAmount)

Increment the phene value by incAmount.

Parameters:

incAmount - The amount by which to increment the phenotype value.

decPheneVal

public void decPheneVal(double decAmount)

Decrement the phene value by incAmount.

Parameters:

decAmount - The amount by which to decrement the phenotype value.

getNumReactants

public int getNumReactants()

Get maximum number of reactants (substrates) that any xholon instance may have in this model.

Returns:

Maximum number of reactants.

setNumReactants

public void setNumReactants(int numR)

Set maximum number of reactants (substrates) that any xholon instance may have in this model.

Parameters:

numR - Maximum number of reactants.

getNumProducts

public int getNumProducts()

Get maximum number of products that any xholon instance may have in this model.

Returns:

Maximum number of products.

setNumProducts

public void setNumProducts(int numP)

Set maximum number of products that any xholon instance may have in this model.

Parameters:

numP - Maximum number of products.

getNumModifiers

public int getNumModifiers()

Get maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.

Returns:

Maximum number of modifiers.

setNumModifiers

public void setNumModifiers(int numM)

Set maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.

Parameters:

numM - Maximum number of modifiers.