org.primordion.cellontro.base
Class BioXholonClass

java.lang.Object
  extended byorg.primordion.xholon.base.Xholon
      extended byorg.primordion.xholon.base.XholonClass
          extended byorg.primordion.cellontro.base.BioXholonClass
All Implemented Interfaces:
IBioXholonClass, IXholon, IXholonClass

public class BioXholonClass
extends XholonClass
implements IBioXholonClass

BioXholonClass is an application specific extension of XholonClass. It encapsulates a geneVal, a featureType, and an activeObjectType.

Since:
0.1 (Created on Oct 12, 2005)
Author:
Ken Webb

Field Summary
 int[] geneVal
           
 boolean reversible
           
 
Fields inherited from class org.primordion.xholon.base.Xholon
DEFAULT_LEVEL, interaction, interactionsEnabled
 
Fields inherited from interface org.primordion.cellontro.base.IBioXholonClass
AOT_BILAYER, AOT_ENZYME, AOT_NULL, AOT_TRANSPORTER, FeatureType_Null, GENEVAL_EFF_KM, GENEVAL_KM, GENEVAL_V, Irr_Sb1_Pr1_Ac0_In0_Co0, Irr_Sb1_Pr1_Ac0_In0_CoN, Irr_Sb1_Pr1_Ac0_In1_CoN, Irr_Sb1_Pr1_Ac1_In0_CoN, Irr_Sb1_Pr1_AcN_InN_CoN, Irr_Sb1_Pr2_Ac0_In0_Co0, Irr_Sb2_Pr1_Ac0_In0_CoN, Rev_Sb1_Pr1_Ac0_In0_Co0, Rev_Sb1_Pr1_Ac0_In0_CoN, Rev_Sb1_Pr2_Ac0_In0_Co0, SIZE_ARRAY_GENEVAL, SIZE_SMCOUNT, SMCOUNT_ACTIVATOR, SMCOUNT_COENZYME, SMCOUNT_INHIBITOR, SMCOUNT_PRODUCT, SMCOUNT_SUBSTRATE
 
Fields inherited from interface org.primordion.xholon.base.IXholonClass
MTYPE_MASK, MtypeActivity, MtypeBraneCalcEntity, MtypeComposition, MtypeConfigContainer, MtypeCtrnnEntity, MtypeGridEntity, MtypeMemCompEntity, MtypePort, MtypeStateMachineEntity, XhtypeActivity, XhtypeBehFgsCon, XhtypeBehFgsxxx, XhtypeBehxxxCon, XhtypeBehxxxxxx, XhtypeBraneCalcEntity, XhtypeBraneCalcEntityActive, XhtypeBraneCalcEntityPassive, XhtypeConfigContainer, XhtypeCtrnnEntity, XhtypeCtrnnEntityActive, XhtypeCtrnnEntityActivePassive, XhtypeGridEntity, XhtypeGridEntityActive, XhtypeGridEntityActivePassive, XhtypeMemCompEntity, XhtypeMemCompEntityActive, XhtypeMemCompEntityActiveContainer, XhtypeMemCompEntityPassive, XhtypeNone, XhtypePort, XhtypePureActiveObject, XhtypePureContainer, XhtypePurePassiveObject, XhtypeStateMachineEntity, XhtypeStateMachineEntityActive, XhtypexxxFgsCon, XhtypexxxFgsxxx, XhtypexxxxxxCon, Xhtypexxxxxxxxx
 
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
BioXholonClass()
          Constructor.
 
Method Summary
 void configure()
          Perform some action, typically once at start up; MAY be overridden.
 int getActiveObjectType()
          Get active object type.
 int getFeatureType()
          Get feature type.
 void initialize()
          Initialize the tree node.
 boolean isReversible()
          Is this reaction reversible.
 void setActiveObjectType(int activeObjectType)
          Set active object type.
 void setFeatureType(int featureType)
          Set feature type.
 void setFeatureType(int[] smCount)
          Set the feature type of an enzyme, based on how many substrates, products, activators, inhibitors, and coenzymes (features) it interacts with.
 java.lang.String toString()
           
 
Methods inherited from class org.primordion.xholon.base.XholonClass
getClassNode, getClassNode, getConfigurationInstructions, getImplName, getInherHier, getMechanismName, getMechanismType, getName, getNextId, getXhType, getXhTypeName, hasAncestor, inOrderPrint, isActiveObject, isContainer, isPassiveObject, postOrderPrint, preOrderPrint, printNode, resetNextId, setImplName, setInherHier, setName, setNavInfo, setXhType
 
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, getNeighbors, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumSiblings, getParentNode, getPort, getPreviousSibling, getRoleName, getRootNode, getSiblings, getSizeMessageQ, 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, handleNodeSelection, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, height, incVal, incVal, initStatics, insertAfter, insertBefore, insertFirstChild, isBound, isExternal, isInternal, isLeaf, isRootNode, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postConfigure, postReconfigure, preAct, preConfigure, preReconfigure, print, println, processMessageQ, processReceivedMessage, reconfigure, remove, removeChild, sendMessage, sendMessage, sendMessage, setAttributeVal, setFactory, setFirstChild, setId, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setPorts, setRoleName, setSizeMessageQ, setUid, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVariableValue, setXhc, swapNode, terminate, 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.IXholonClass
getConfigurationInstructions, getImplName, getXhType, hasAncestor, inOrderPrint, postOrderPrint, preOrderPrint, setImplName, setName, setNavInfo, setXhType
 
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, 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, handleNodeSelection, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, height, incVal, incVal, initStatics, insertAfter, insertBefore, insertFirstChild, isActiveObject, isBound, isContainer, isExternal, isInternal, isLeaf, isPassiveObject, isRootNode, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postConfigure, postReconfigure, preAct, preConfigure, 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
 

Field Detail

reversible

public boolean reversible

geneVal

public int[] geneVal
Constructor Detail

BioXholonClass

public BioXholonClass()
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 XholonClass

getFeatureType

public int getFeatureType()
Description copied from interface: IBioXholonClass
Get feature type.

Specified by:
getFeatureType in interface IBioXholonClass
Returns:
The feature type.

setFeatureType

public void setFeatureType(int featureType)
Description copied from interface: IBioXholonClass
Set feature type.

Specified by:
setFeatureType in interface IBioXholonClass
Parameters:
featureType - The feature type.

isReversible

public boolean isReversible()
Description copied from interface: IBioXholonClass
Is this reaction reversible.

Specified by:
isReversible in interface IBioXholonClass
Returns:
true or false

setFeatureType

public void setFeatureType(int[] smCount)
Description copied from interface: IBioXholonClass
Set the feature type of an enzyme, based on how many substrates, products, activators, inhibitors, and coenzymes (features) it interacts with.

Specified by:
setFeatureType in interface IBioXholonClass
Parameters:
smCount - An array containing a count of various features.

getActiveObjectType

public int getActiveObjectType()
Description copied from interface: IBioXholonClass
Get active object type.

Specified by:
getActiveObjectType in interface IBioXholonClass
Returns:
The active object type.

setActiveObjectType

public void setActiveObjectType(int activeObjectType)
Description copied from interface: IBioXholonClass
Set active object type.

Specified by:
setActiveObjectType in interface IBioXholonClass
Parameters:
activeObjectType - The active object type.

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 XholonClass

toString

public java.lang.String toString()
Overrides:
toString in class XholonClass