main
Class Node

java.lang.Object
  main.Node

All Implemented Interfaces:

java.lang.Cloneable

Direct Known Subclasses:

CalculatorNode

public class Node

extends java.lang.Object

implements java.lang.Cloneable

A node is one of the state variables in the model: an mRNA, protein, protein complex, protein at a membrane, etc. Each node contains a set of Affectors which specify how that node changes over time. A copy of each type of node is put into each cell.

Note - you can't use a freshly made node. You must use a copy of the node, because copying the node fixes the array of affectors (the original uses affectorVector so that it is easy to build).

Field Summary

Affector[]	affectors
int	numSides
int	this_debug_num

Method Summary

void	addExpAffector(Affector aff, Cell cell)
Node	copy()
void	getAffectorsValue(float[] vals)
float	getAffectorsValue(int side)
float	getIntegrationValue()
float	getIntegrationValue(int side)
int	getNodeNum()
float	getNoise()
int	getNumAffectors()
void	getSeparatedDeriv(float[] fhat_vals, float[] dfdyi_vals)
float	getSum()
void	getValue(float[] vals)
float	getValue(int side)
protected void	init(int node_num)
void	removeExpAffectors()
void	setAffectors(java.util.Vector affector_templates, Cell cell)
void	setFinalValues(float[] vals)
void	setIntegrationValues(float[] vals)
void	setNoise(float amplitude)
void	setNumSides(int num_sides)
void	setValue(float val)
void	setValue(int side, float val)
void	setValue(NodeValues newvalues)

Methods inherited from class java.lang.Object

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

Field Detail

numSides

public int numSides

affectors

public Affector[] affectors

this_debug_num

public int this_debug_num

Method Detail

setAffectors

public void setAffectors(java.util.Vector affector_templates,
                         Cell cell)
                  throws java.lang.Exception

Throws:

java.lang.Exception

init

protected void init(int node_num)

setNumSides

public void setNumSides(int num_sides)

getAffectorsValue

public final float getAffectorsValue(int side)

getAffectorsValue

public final void getAffectorsValue(float[] vals)

getSeparatedDeriv

public final void getSeparatedDeriv(float[] fhat_vals,
                                    float[] dfdyi_vals)

getIntegrationValue

public float getIntegrationValue()

getIntegrationValue

public float getIntegrationValue(int side)

setIntegrationValues

public void setIntegrationValues(float[] vals)

setFinalValues

public void setFinalValues(float[] vals)

getValue

public float getValue(int side)

getValue

public void getValue(float[] vals)

getSum

public float getSum()

setValue

public void setValue(float val)

setValue

public void setValue(int side,
                     float val)

setValue

public void setValue(NodeValues newvalues)

getNoise

public float getNoise()

setNoise

public void setNoise(float amplitude)

getNodeNum

public int getNodeNum()

getNumAffectors

public int getNumAffectors()

copy

public Node copy()

addExpAffector

public void addExpAffector(Affector aff,
                           Cell cell)
                    throws java.lang.Exception

Throws:

java.lang.Exception

removeExpAffectors

public void removeExpAffectors()