EEXIST

java.lang.Object
- com.cellmatrix.chemcomp.API.v1.EEXIST

```
public class EEXIST
extends java.lang.Object
```
Version:

1.0 API for EEXIST (Egoless EXtened effect contInuous Space Time system)
A series of methods and fields for simulating the behavior of an EEXIST system

Author:

Nicholas J. Macias, Cell Matrix Corporation

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`Absolute` chemical values specify absolute coordinates
`static int`	`DST` index used to specify destination chemical
`static int`	`Relative` chemical values specify relative coordinates
`static int`	`SRC` index used to specify source chemical

Constructor Summary

Constructors
Constructor and Description
`EEXIST()` constructor with no arguments uses minX=0, maxX=40, dx=0.0625
`EEXIST(double minX, double maxX, double dx)` main class for EEXIST system

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`clearAllTubes()` zero-out all tubes.
`double[][]`	`getAllBiass()` read all bias levels
`double[][]`	`getAllTubes()` read all chemical levels
`double`	`getDx()` read (fixed) spatial increment (dx)
`double`	`getKarma()` returns the current karma of each transfer
`double`	`getMaxX()` read (fixed) maximum X value (tube n)
`double`	`getMinX()` read (fixed) minimum X value (tube 0)
`int`	`getTimeStep()` How many simulated time steps have passed since the last reset
`double`	`getTube(double x, int SD)` read the amount of SRC or DST chemical in a tube
`void`	`loadIndividual(Individual indiv)` load an individual into the system
`void`	`localPaint()` Draw into buffered image, then display in main display window Also update graphFrame (detail display)
`int`	`numTubes()` Return number of tubes
`void`	`proportionalFlow(boolean state)` Control whether flow rate is based on current chemical level
`void`	`releaseDisplay()` de-associate a display from an EEXIST.
`void`	`resetTimeStep()` Reset the internal timeclock to t=0
`void`	`saveDisplay(Display d)` associate a display with this EEXIST.
`void`	`setAllBiass(double[][] bias)` load all bias values from 2D array
`void`	`setAllDiameters(double[] diameters)` set all tube diameters from an array of values
`void`	`setAllTubes(double[][] mem)` load all SRC/DST values from 2-D array
`void`	`setBias(double xLoc, int sd, double biasVal)` set SRC/DST deltas (added to chemical levels to choose src/dst addresses)
`void`	`setBias(int tube, int sd, double biasVal)` set bias value for a given tube (integer index)
`void`	`setDiameter(double xLoc, double diameter)` set diameter of a tube biasd on its spatial coordinates
`void`	`setDiameter(int tube, double diameter)` set diameter of a single tube
`void`	`setDt(double dt)` Set timestep for simulation (default=0.05)
`void`	`setKarma(double karma)` Set karma (interlinking of cause and effect) of transfers.
`void`	`setTransferMode(int mode)` Set the mode for chemical transfers.
`void`	`setTube(double x, int SD, double value)` set a tube's contents
`void`	`setTube(int tube, int SD, double value)` set a tube's contents
`void`	`step(int steps)` advance the simulation a number of steps

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - SRC
```
public static int SRC
```
    index used to specify source chemical
  - DST
```
public static int DST
```
    index used to specify destination chemical
  - Absolute
```
public static final int Absolute
```
    chemical values specify absolute coordinates
    
    See Also:
    
    Constant Field Values
  - Relative
```
public static final int Relative
```
    chemical values specify relative coordinates
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - EEXIST
```
public EEXIST()
```
    constructor with no arguments uses minX=0, maxX=40, dx=0.0625
  - EEXIST
```
public EEXIST(double minX,
              double maxX,
              double dx)
```
    main class for EEXIST system
    
    Parameters:
    
    minX - smallest bin number
    
    maxX - largest bin number
    
    dx - spatial increment
- Method Detail
  - proportionalFlow
```
public void proportionalFlow(boolean state)
```
    Control whether flow rate is based on current chemical level
    
    Parameters:
    
    state - - set true to make flow rate proportional to current chemical level
  - setDt
```
public void setDt(double dt)
```
    Set timestep for simulation (default=0.05)
    
    Parameters:
    
    dt - specifies the timestep
  - setKarma
```
public void setKarma(double karma)
```
    Set karma (interlinking of cause and effect) of transfers. Transfers centered at a location of x will also occur nearby. The diameter of the transfer conduit drops off linearly, from 1 (max) at the original coordinate, to 0 (min) at a distance of "karma."
    
    Parameters:
    
    karma - is the spatial extent of the transfer's karma
  - getKarma
```
public double getKarma()
```
    returns the current karma of each transfer
    
    Returns:
    
    current karma
  - setAllDiameters
```
public void setAllDiameters(double[] diameters)
```
    set all tube diameters from an array of values
    
    Parameters:
    
    diameters - array of tube diameters [0,binMax]
  - setDiameter
```
public void setDiameter(int tube,
                        double diameter)
```
    set diameter of a single tube
    
    Parameters:
    
    tube - integer tube number [0,binMax]
    
    diameter - diameter to set
  - setDiameter
```
public void setDiameter(double xLoc,
                        double diameter)
```
    set diameter of a tube biasd on its spatial coordinates
    
    Parameters:
    
    xLoc - X location of the tube
    
    diameter - diameter to set
  - setBias
```
public void setBias(int tube,
                    int sd,
                    double biasVal)
```
    set bias value for a given tube (integer index)
    
    Parameters:
    
    tube - index of tube to set
    
    sd - EEXIST.SRC or EEXIST.DST
    
    biasVal - delta (default 0)
  - setBias
```
public void setBias(double xLoc,
                    int sd,
                    double biasVal)
```
    set SRC/DST deltas (added to chemical levels to choose src/dst addresses)
    
    Parameters:
    
    xLoc - spatial location of tube
    
    sd - EEXIST.SRC or SSXIST.DST
    
    biasVal - delta (default 0)
  - setAllBiass
```
public void setAllBiass(double[][] bias)
```
    load all bias values from 2D array
    
    Parameters:
    
    bias - 2-D array of bias values: [x][SRC/DST]
  - setTransferMode
```
public void setTransferMode(int mode)
```
    Set the mode for chemical transfers.
    
    Parameters:
    
    mode - specifies the type of transfers that take place. Options are:
    EEXIST.Absolute - values are treated as absolute spatial coordinates
    EEXIST.Relative - values are treated as displacements from the current location (+/-) This should be changed sometime to allow for negative displacements.
  - resetTimeStep
```
public void resetTimeStep()
```
    Reset the internal timeclock to t=0
  - getTimeStep
```
public int getTimeStep()
```
    How many simulated time steps have passed since the last reset
    
    Returns:
    
    Number of time steps
  - getMinX
```
public double getMinX()
```
    read (fixed) minimum X value (tube 0)
    
    Returns:
    
    minimum X value
  - getMaxX
```
public double getMaxX()
```
    read (fixed) maximum X value (tube n)
    
    Returns:
    
    maximum X value
  - getDx
```
public double getDx()
```
    read (fixed) spatial increment (dx)
    
    Returns:
    
    dx
  - saveDisplay
```
public void saveDisplay(Display d)
```
    associate a display with this EEXIST. step() will record activity for the display to paint
    
    Parameters:
    
    d - Display object to link to this EEXIST
  - releaseDisplay
```
public void releaseDisplay()
```
    de-associate a display from an EEXIST. The Display itself is not affected by this.
  - numTubes
```
public int numTubes()
```
    Return number of tubes
    
    Returns:
    
    number of tubes
  - loadIndividual
```
public void loadIndividual(Individual indiv)
```
    load an individual into the system
    
    Parameters:
    
    indiv - the individual to load. indiv's contents will completely replace the contents of the EEXIST system's tubes
  - setTube
```
public void setTube(int tube,
                    int SD,
                    double value)
```
    set a tube's contents
    
    Parameters:
    
    tube - tube's number (integer index)
    
    SD - EEXIST.SRC or EEXIST.DST
    
    value - total amount of SRC or DST chemical to store in tube
  - setTube
```
public void setTube(double x,
                    int SD,
                    double value)
```
    set a tube's contents
    
    Parameters:
    
    x - tube's x coordinate
    
    SD - EEXIST.SRC or EEXIST.DST
    
    value - total amount of SRC or DST chemical to store in tube
  - setAllTubes
```
public void setAllTubes(double[][] mem)
```
    load all SRC/DST values from 2-D array
    
    Parameters:
    
    mem - array of values. [x][SRC/DST]
  - getTube
```
public double getTube(double x,
                      int SD)
```
    read the amount of SRC or DST chemical in a tube
    
    Parameters:
    
    x - tube's x coordinate
    
    SD - EEXIST.SRC or EEXIST.DST
    
    Returns:
    
    total amount of SRC or DST chemical in tube
  - getAllTubes
```
public double[][] getAllTubes()
```
    read all chemical levels
    
    Returns:
    
    2D array of chemical values, suitable for setAllTubes
  - getAllBiass
```
public double[][] getAllBiass()
```
    read all bias levels
    
    Returns:
    
    2D array of bias levels, suitable for setAllBiass
  - clearAllTubes
```
public void clearAllTubes()
```
    zero-out all tubes. This properly belongs more to the Individual class than the EEXIST class
  - step
```
public void step(int steps)
```
    advance the simulation a number of steps
    
    Parameters:
    
    steps - number of timesteps (dt each)
  - localPaint
```
public void localPaint()
```
    Draw into buffered image, then display in main display window Also update graphFrame (detail display)

Class EEXIST

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SRC

DST

Absolute

Relative

Constructor Detail

EEXIST

EEXIST

Method Detail

proportionalFlow

setDt

setKarma

getKarma

setAllDiameters

setDiameter

setDiameter

setBias

setBias

setAllBiass

setTransferMode

resetTimeStep

getTimeStep

getMinX

getMaxX

getDx

saveDisplay

releaseDisplay

numTubes

loadIndividual

setTube

setTube

setAllTubes

getTube

getAllTubes

getAllBiass

clearAllTubes

step

localPaint