main
Class Cell

java.lang.Object
  main.Cell

public class Cell

extends java.lang.Object

This class represents a single cell in the model. Each cell stores its own set of nodes (rna and protein types), and can have separate nodes for each side of the cell. Cells are involved in setting up the model, but once the model is set up they are not very involved in integrating - they just call their nodes to do the integration. One future addition we need to make is to get cells so that they can dynamically switch neighbors.

Nested Class Summary

class	Cell.Hexagon An internal class used for generating hexagonal cell shape
class	Cell.Square An internal class used for generating square cell shape

Field Summary

static int	arrayHeight
static int	arrayWidth
Cell[]	neighbors The cell's neighbors - set up by the init object
Node[]	nodes

Constructor Summary

Cell(float x, float y)
Main constructor

Method Summary

void	addAffectors(Network net)
void	addExperimentToNode(java.lang.String nodename, Affector aff)
void	addNeighbor(Cell neighbor)
void	addNodes(Network net)
void	clearExperiment()
java.awt.Polygon	getCellShape() Returns the cells shape.
float	getInitialValue(int nodeNum)
float	getInitialValue(java.lang.String nodename)
int	getItsNum()
Node	getNeighborNode(int side, java.lang.String name)
Node	getNode(java.lang.String name)
int	getNodeNum(java.lang.String name)
float	getValue(int node_num)
float[]	getValues() Returns all the node values for a cell in the form of an array of floats
void	init()
void	init(boolean from_last_state) initialize network from a stored previous state (if from_last_state == true) else from stored ICs
float	nodePeek(java.lang.String name)
void	save(java.io.PrintWriter out)
void	saveHeadings(java.io.PrintWriter out)
void	setInitialValue(int nodeNum, float val)
void	setInitialValue(java.lang.String nodename, float val)
protected void	setItsNum(int n)
void	setLocation(java.awt.geom.Point2D.Float location) Sets the location of the cell
void	setValue(int node_num, float val)
void	setValue(java.lang.String nodename, float val)

Methods inherited from class java.lang.Object

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

Field Detail

arrayWidth

public static int arrayWidth

arrayHeight

public static int arrayHeight

neighbors

public Cell[] neighbors

The cell's neighbors - set up by the init object

nodes

public Node[] nodes

Constructor Detail

Cell

public Cell(float x,
            float y)

Main constructor

Method Detail

setItsNum

protected void setItsNum(int n)

getItsNum

public int getItsNum()

save

public void save(java.io.PrintWriter out)

saveHeadings

public void saveHeadings(java.io.PrintWriter out)

addNodes

public void addNodes(Network net)

addAffectors

public void addAffectors(Network net)
                  throws java.lang.Exception

Throws:

java.lang.Exception

addNeighbor

public void addNeighbor(Cell neighbor)

getCellShape

public java.awt.Polygon getCellShape()

Returns the cells shape.

Returns:

Polygon - The shape of the cell.

getNeighborNode

public Node getNeighborNode(int side,
                            java.lang.String name)
                     throws java.lang.Exception

Throws:

java.lang.Exception

getNode

public Node getNode(java.lang.String name)
             throws java.lang.Exception

Throws:

java.lang.Exception

getNodeNum

public int getNodeNum(java.lang.String name)
               throws java.lang.Exception

Throws:

java.lang.Exception

setInitialValue

public void setInitialValue(java.lang.String nodename,
                            float val)
                     throws java.lang.Exception

Throws:

java.lang.Exception

setInitialValue

public void setInitialValue(int nodeNum,
                            float val)

getInitialValue

public float getInitialValue(java.lang.String nodename)
                      throws java.lang.Exception

Throws:

java.lang.Exception

getInitialValue

public float getInitialValue(int nodeNum)

addExperimentToNode

public void addExperimentToNode(java.lang.String nodename,
                                Affector aff)

clearExperiment

public void clearExperiment()

nodePeek

public float nodePeek(java.lang.String name)

init

public void init()

init

public void init(boolean from_last_state)

initialize network from a stored previous state (if from_last_state == true) else from stored ICs

getValue

public float getValue(int node_num)

getValues

public float[] getValues()

Returns all the node values for a cell in the form of an array of floats

Returns:

float[]

setValue

public void setValue(int node_num,
                     float val)

setValue

public void setValue(java.lang.String nodename,
                     float val)
              throws java.lang.Exception

Throws:

java.lang.Exception

setLocation

public void setLocation(java.awt.geom.Point2D.Float location)

Sets the location of the cell