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.