org.primordion.cellontro.base
Interface IBioXholonClass

All Superinterfaces:

IXholon, IXholonClass

All Known Implementing Classes:

BioXholonClass

public interface IBioXholonClass

extends IXholonClass

Field Summary

static int	AOT_BILAYER
static int	AOT_ENZYME
static int	AOT_NULL
static int	AOT_TRANSPORTER
static int	FeatureType_Null
static int	GENEVAL_EFF_KM
static int	GENEVAL_KM
static int	GENEVAL_V
static int	Irr_Sb1_Pr1_Ac0_In0_Co0
static int	Irr_Sb1_Pr1_Ac0_In0_CoN
static int	Irr_Sb1_Pr1_Ac0_In1_CoN
static int	Irr_Sb1_Pr1_Ac1_In0_CoN
static int	Irr_Sb1_Pr1_AcN_InN_CoN
static int	Irr_Sb1_Pr2_Ac0_In0_Co0
static int	Irr_Sb2_Pr1_Ac0_In0_CoN
static int	Rev_Sb1_Pr1_Ac0_In0_Co0
static int	Rev_Sb1_Pr1_Ac0_In0_CoN
static int	Rev_Sb1_Pr2_Ac0_In0_Co0
static int	SIZE_ARRAY_GENEVAL
static int	SIZE_SMCOUNT
static int	SMCOUNT_ACTIVATOR
static int	SMCOUNT_COENZYME
static int	SMCOUNT_INHIBITOR
static int	SMCOUNT_PRODUCT
static int	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

Method Summary

int	getActiveObjectType() Get active object type.
int	getFeatureType() Get feature type.
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.

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, 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, initialize, 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

FeatureType_Null

public static final int FeatureType_Null

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Constant Field Values

Irr_Sb1_Pr1_Ac0_In0_Co0

public static final int Irr_Sb1_Pr1_Ac0_In0_Co0

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Irr_Sb1_Pr2_Ac0_In0_Co0

public static final int Irr_Sb1_Pr2_Ac0_In0_Co0

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Irr_Sb1_Pr1_Ac0_In0_CoN

public static final int Irr_Sb1_Pr1_Ac0_In0_CoN

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Irr_Sb2_Pr1_Ac0_In0_CoN

public static final int Irr_Sb2_Pr1_Ac0_In0_CoN

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Irr_Sb1_Pr1_Ac0_In1_CoN

public static final int Irr_Sb1_Pr1_Ac0_In1_CoN

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Irr_Sb1_Pr1_Ac1_In0_CoN

public static final int Irr_Sb1_Pr1_Ac1_In0_CoN

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Irr_Sb1_Pr1_AcN_InN_CoN

public static final int Irr_Sb1_Pr1_AcN_InN_CoN

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Rev_Sb1_Pr1_Ac0_In0_Co0

public static final int Rev_Sb1_Pr1_Ac0_In0_Co0

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Rev_Sb1_Pr1_Ac0_In0_CoN

public static final int Rev_Sb1_Pr1_Ac0_In0_CoN

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Rev_Sb1_Pr2_Ac0_In0_Co0

public static final int Rev_Sb1_Pr2_Ac0_In0_Co0

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SMCOUNT_SUBSTRATE

public static final int SMCOUNT_SUBSTRATE

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SMCOUNT_PRODUCT

public static final int SMCOUNT_PRODUCT

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SMCOUNT_ACTIVATOR

public static final int SMCOUNT_ACTIVATOR

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SMCOUNT_INHIBITOR

public static final int SMCOUNT_INHIBITOR

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SMCOUNT_COENZYME

public static final int SMCOUNT_COENZYME

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Constant Field Values

SIZE_SMCOUNT

public static final int SIZE_SMCOUNT

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Constant Field Values

AOT_NULL

public static final int AOT_NULL

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AOT_ENZYME

public static final int AOT_ENZYME

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Constant Field Values

AOT_BILAYER

public static final int AOT_BILAYER

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AOT_TRANSPORTER

public static final int AOT_TRANSPORTER

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Constant Field Values

GENEVAL_KM

public static final int GENEVAL_KM

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GENEVAL_V

public static final int GENEVAL_V

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GENEVAL_EFF_KM

public static final int GENEVAL_EFF_KM

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SIZE_ARRAY_GENEVAL

public static final int SIZE_ARRAY_GENEVAL

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Constant Field Values

Method Detail

getFeatureType

public int getFeatureType()

Get feature type.

Returns:

The feature type.

setFeatureType

public void setFeatureType(int featureType)

Set feature type.

Parameters:

featureType - The feature type.

isReversible

public boolean isReversible()

Is this reaction reversible.

Returns:

true or false

setFeatureType

public 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.

Parameters:

smCount - An array containing a count of various features.

getActiveObjectType

public int getActiveObjectType()

Get active object type.

Returns:

The active object type.

setActiveObjectType

public void setActiveObjectType(int activeObjectType)

Set active object type.

Parameters:

activeObjectType - The active object type.