affectors
Class Affector

java.lang.Object
  affectors.Affector

All Implemented Interfaces:

java.lang.Cloneable

Direct Known Subclasses:

Affector_Template, Cleavage2A_ICAff, Cleavage2B_ICAff, CleavageA_ECAff, CleavageA_ICAff, CleavageA_ICDipAff, CleavageB_ECAff, CleavageB_ICAff, CleavageB_ICDipAff, CleaveA_Aff, CleaveB_Aff, CompAct2Aff, ConstantInputAff, ConstantLevelAff, ConversionEAff, ConversionIAff, DecayAff, DecayRegDownAff, DecayRegUpAff, DefinedValuesAff, DefinedValuesIndicatorAff, Dephosphor1StepA_ICAff, Dephosphor1StepB_ICAff, DephosphorylateA_Aff, DephosphorylateB_Aff, DephosphorylationA_ICAff, DephosphorylationB_ICAff, Dimerize_AAff, Dimerize_BAff, DimerizeAllMembrane_AAff, DimerizeAllMembrane_BAff, DimerizeCrossMembrane_AAff, DimerizeCrossMembrane_BAff, DimerizeCytoMem_AAff, DimerizeCytoMem_BAff, DimerizeCytoMem_CAff, DimerizeMemCyto_AAff, DimerizeMemCyto_BAff, DimerizeMemCyto_CAff, DissociationA_Aff, DissociationB_Aff, DissociationC_Aff, DissociationCytoMemA_Aff, DissociationCytoMemB_Aff, DissociationCytoMemC_Aff, DissociationEC_Com_Aff, DissociationEC_Lig_Aff, DissociationEC_Rec_Aff, EndoEAff, EndoIAff, EnhancerRegionAff, EnzymeConversionEC_Pro_Aff, EnzymeConversionEC_Sub_Aff, ExoEAff, ExoIAff, Formula1Aff, HeatShockAff, LMxferEAff, LMxferIAff, MxferInAff, MxferOutAff, NoChangeAff, Phosphor1StepA_ICAff, Phosphor1StepB_ICAff, PhosphorylateA_Aff, PhosphorylateB_Aff, PhosphorylationA_ICAff, PhosphorylationB_ICAff, PlaceHolderAff, PsiAff, PsiECAff, RecycleAAff, RecycleBAff, TlnAff, TlnRegUpAff, Txn1Aff, Txn1ECAff, Txn2aAff, Txn2aDipAff, Txn2bAff, Txn2bDipAff, Txn3aAff, Txn3bAff, Txn4Aff, Txn4DipAff, Txn5Aff, Txn6aAff, Txn6bAff, TxnLeakyCyceAff, TxnSiteActInhibit2Aff, TxnSiteActInhibit3Aff, TxnSiteActInhibitAff, TxnSiteActivatorAff, TxnSiteAddInhibitorAff, TxnSiteInhibitorAff, VonForresterA_Aff, VonForresterA_ECAff, VonForresterA_ICAff, VonForresterB_Aff, VonForresterB_ECAff, VonForresterB_ICAff, WhiteNoiseAff, XferInAff, XferOutAff

public abstract class Affector

extends java.lang.Object

implements java.lang.Cloneable

Stores the formula for how a node changes over time. Each affector encapsulates a particular bit of the full formula for each node, generally an additive term of the differential equation. The base class Affector also stores the current values of all the parameters in the model.

Field Summary

java.lang.String	ADesc Descriptors for use by the GUI; set these to point to static final Strings that say in as few words as possible what the Affector does (ADesc), what nodes need to be specified (NDesc), and what parameters it uses (PDesc).
int	affectorType
static int	CC Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.
static int	CERTIFICATION Position meanings for Type[].
static int	CONVERSION Type.[TERMTYPE] values;
float	copyNumber
static int	DEGRADATION Type.[TERMTYPE] values;
static int	FF Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.
static int	firstFreeParam
static int	GG Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.
static int	GUI_CAPABLE Position meanings for Type[].
static int	HH Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.
static int	KK Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.
static int	MATHTYPE Position meanings for Type[].
java.lang.String[]	NDesc
java.lang.String[]	PDesc
static int	PRODUCTION Type.[TERMTYPE] values;
static int	RETURNS_DERIV Type.[CERTIFICATION] values; in the constructor of a subclass, once you have made sure the formula in getValue (and getNCValue if necessary) is correct, set this.Type.[CERTIFICATION]=Affector.RETURNS_DERIV, and once your subclass knows how to return a list of partial derivatives, set it to RETURNS_PARTIALS.
static int	RETURNS_PARTIALS Type.[CERTIFICATION] values; in the constructor of a subclass, once you have made sure the formula in getValue (and getNCValue if necessary) is correct, set this.Type.[CERTIFICATION]=Affector.RETURNS_DERIV, and once your subclass knows how to return a list of partial derivatives, set it to RETURNS_PARTIALS.
static int	TERMTYPE Position meanings for Type[].
static int	TT Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.
int[]	Type The Type array is public only so it can be read without the cost of a method call...
static int	UNSPECIFIED Type.[] default value.

Method Summary

static void	addDefaultParam(java.lang.String name, float val, float low, float high, java.lang.String variation)
float	Chi(float M, float K, float nu)
static void	clearStatic()
void	copy_(Affector cp)
Affector	copy()
boolean	doesContainTarget(Node which_node)
static int	findOrCreateParam(java.lang.String name) for use of the CalculatorNode or other things that need to look up parameters if they already exist but make them if they do not...
static int	findParam(java.lang.String name)
void	fixNodes(Cell cell, java.lang.String[] node_names)
float	getNCValue(Node which_node)
Node[]	getNodes() This function is here so that viewers can examine an affector.
int	getNumNodes()
int	getNumParameters()
static int	getOtherSide(int side)
static Parameter	getParameter(int pos) Use this to read a Parameter object, identified by number, from the static arrays held by Affector.
static Parameter	getParameter(java.lang.String name) Use this to read a Parameter object, identified by name, from the static arrays held by Affector.
static java.lang.String	getParamName(int pos)
static int	getParamPos(java.lang.String name) This function should only be called when constructing a model from the init() function of an iterator.
static float	getParamValue(int pos) Use this instead of getting a whole Parameter object if all you want is the value of a parameter identified by its position.
static float	getParamValue(java.lang.String name) Use this instead of getting a whole Parameter object if all you want is the named parameter's value.
static int	getParamVariationMode(int pos)
float	getValue(Node which_node)
void	init(int side, int num_params, java.lang.String[] params)
boolean	isLinearInTarget()
float	Phi(float M, float K, float nu)
float	Psi(float M, float K, float nu)
protected void	setContainsTarget(boolean b)
protected void	setDescriptions(java.lang.String aff_desc, java.lang.String[] node_desc, java.lang.String[] param_desc)
protected abstract void	setLabelsAndTypes()
static void	setParameter(Parameter p) Use this to set a parameter using a Parameter object.
abstract void	setParameterNumbers(int[] param_nums)
static void	setParamRange(java.lang.String name, float lower, float upper, int mode)
static void	setParamRange(java.lang.String name, float lower, float upper, java.lang.String mode)
static void	setParamValue(int param_pos, float val)
static void	setParamValue(java.lang.String name, float val)
void	setSide(int side)
protected void	setSided(boolean sided, int[] which_sides)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

firstFreeParam

public static int firstFreeParam

copyNumber

public float copyNumber

affectorType

public int affectorType

Type

public int[] Type

The Type array is public only so it can be read without the cost of a method call... NO ONE should set any value in this array except in the constructor of and Affector subclass, and then only when you know what you're doing.

TERMTYPE

public static final int TERMTYPE

Position meanings for Type[].

See Also:

Constant Field Values

MATHTYPE

public static final int MATHTYPE

Position meanings for Type[].

See Also:

Constant Field Values

CERTIFICATION

public static final int CERTIFICATION

Position meanings for Type[].

See Also:

Constant Field Values

GUI_CAPABLE

public static final int GUI_CAPABLE

Position meanings for Type[].

See Also:

Constant Field Values

UNSPECIFIED

public static final int UNSPECIFIED

Type.[] default value.

See Also:

Constant Field Values

FF

public static final int FF

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

See Also:

Constant Field Values

GG

public static final int GG

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

See Also:

Constant Field Values

HH

public static final int HH

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

See Also:

Constant Field Values

KK

public static final int KK

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

See Also:

Constant Field Values

CC

public static final int CC

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

See Also:

Constant Field Values

TT

public static final int TT

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

See Also:

Constant Field Values

PRODUCTION

public static final int PRODUCTION

Type.[TERMTYPE] values;

See Also:

Constant Field Values

CONVERSION

public static final int CONVERSION

Type.[TERMTYPE] values;

See Also:

Constant Field Values

DEGRADATION

public static final int DEGRADATION

Type.[TERMTYPE] values;

See Also:

Constant Field Values

RETURNS_DERIV

public static final int RETURNS_DERIV

Type.[CERTIFICATION] values; in the constructor of a subclass, once you have made sure the formula in getValue (and getNCValue if necessary) is correct, set this.Type.[CERTIFICATION]=Affector.RETURNS_DERIV, and once your subclass knows how to return a list of partial derivatives, set it to RETURNS_PARTIALS.

See Also:

Constant Field Values

RETURNS_PARTIALS

public static final int RETURNS_PARTIALS

Type.[CERTIFICATION] values; in the constructor of a subclass, once you have made sure the formula in getValue (and getNCValue if necessary) is correct, set this.Type.[CERTIFICATION]=Affector.RETURNS_DERIV, and once your subclass knows how to return a list of partial derivatives, set it to RETURNS_PARTIALS.

See Also:

Constant Field Values

ADesc

public java.lang.String ADesc

Descriptors for use by the GUI; set these to point to static final Strings that say in as few words as possible what the Affector does (ADesc), what nodes need to be specified (NDesc), and what parameters it uses (PDesc). Once your Affector subclass does all this, set this.Type.[GUI_CAPABLE]=1

NDesc

public java.lang.String[] NDesc

PDesc

public java.lang.String[] PDesc

Method Detail

clearStatic

public static void clearStatic()

setLabelsAndTypes

protected abstract void setLabelsAndTypes()

setParameterNumbers

public abstract void setParameterNumbers(int[] param_nums)

getNumNodes

public int getNumNodes()

getNumParameters

public int getNumParameters()

init

public void init(int side,
                 int num_params,
                 java.lang.String[] params)

setDescriptions

protected void setDescriptions(java.lang.String aff_desc,
                               java.lang.String[] node_desc,
                               java.lang.String[] param_desc)

setSided

protected void setSided(boolean sided,
                        int[] which_sides)

setSide

public void setSide(int side)

setContainsTarget

protected void setContainsTarget(boolean b)

isLinearInTarget

public boolean isLinearInTarget()

getValue

public float getValue(Node which_node)

getNCValue

public float getNCValue(Node which_node)

doesContainTarget

public boolean doesContainTarget(Node which_node)

copy_

public void copy_(Affector cp)

copy

public Affector copy()

fixNodes

public void fixNodes(Cell cell,
                     java.lang.String[] node_names)
              throws java.lang.Exception

Throws:

java.lang.Exception

getOtherSide

public static int getOtherSide(int side)

Phi

public final float Phi(float M,
                       float K,
                       float nu)

Psi

public final float Psi(float M,
                       float K,
                       float nu)

Chi

public final float Chi(float M,
                       float K,
                       float nu)

findParam

public static int findParam(java.lang.String name)
                     throws java.lang.Exception

Throws:

java.lang.Exception

findOrCreateParam

public static int findOrCreateParam(java.lang.String name)
                             throws java.lang.Exception

for use of the CalculatorNode or other things that need to look up parameters if they already exist but make them if they do not... mimics getParamPos. Use with care.

Throws:

java.lang.Exception

getParamPos

public static int getParamPos(java.lang.String name)
                       throws java.lang.Exception

This function should only be called when constructing a model from the init() function of an iterator. If called from other places, it may screw stuff up.

Throws:

java.lang.Exception

getParamName

public static java.lang.String getParamName(int pos)

getParamVariationMode

public static int getParamVariationMode(int pos)

setParamRange

public static void setParamRange(java.lang.String name,
                                 float lower,
                                 float upper,
                                 java.lang.String mode)
                          throws java.lang.Exception

Throws:

java.lang.Exception

setParamRange

public static void setParamRange(java.lang.String name,
                                 float lower,
                                 float upper,
                                 int mode)

getParameter

public static Parameter getParameter(java.lang.String name)

Use this to read a Parameter object, identified by name, from the static arrays held by Affector.

getParameter

public static Parameter getParameter(int pos)

Use this to read a Parameter object, identified by number, from the static arrays held by Affector.

setParameter

public static void setParameter(Parameter p)

Use this to set a parameter using a Parameter object.

getParamValue

public static float getParamValue(int pos)

Use this instead of getting a whole Parameter object if all you want is the value of a parameter identified by its position.

getParamValue

public static float getParamValue(java.lang.String name)
                           throws java.lang.Exception

Use this instead of getting a whole Parameter object if all you want is the named parameter's value.

Throws:

java.lang.Exception

setParamValue

public static void setParamValue(java.lang.String name,
                                 float val)

setParamValue

public static void setParamValue(int param_pos,
                                 float val)

addDefaultParam

public static void addDefaultParam(java.lang.String name,
                                   float val,
                                   float low,
                                   float high,
                                   java.lang.String variation)
                            throws java.lang.Exception

Throws:

java.lang.Exception

getNodes

public Node[] getNodes()

This function is here so that viewers can examine an affector. They should not be used by any of the modeling classes themselves.