ca.cas.montecarlo
Class CircleIrradiator

java.lang.Object
  ca.cas.montecarlo.Irradiator
      ca.cas.montecarlo.CircleIrradiator

public class CircleIrradiator
extends Irradiator

Each CircleIrradiator object represents the process in which a genome arranged as a CircleGeometry is irradiated and double strand breaks occur.

Field Summary

Fields inherited from class ca.cas.montecarlo.Irradiator

breaks

Constructor Summary

CircleIrradiator(double alpha, ProbDist sec, ProbDist c)
Constructs a CircleIrradiator object

Method Summary

Break[]	breaks() Returns an array of the double strand breaks that occur during the course of the irradiation of the genome
void	irradiate(java.util.Random rGen) Calling this method causes the irradiator class to generate a new array of Breaks in the Geometry set by setGeometry().
void	setGeometry(Geometry geo) This method is intended to be used by the driver to specify the Geometry object which should be used as a basis for this irradiation process.
int	sizeOfPrimary() Returns the number of points in the primary process
int	sizeOfSecondary() Returns the number of points in the secondary process

Methods inherited from class java.lang.Object

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

Constructor Detail

CircleIrradiator

public CircleIrradiator(double alpha,
                        ProbDist sec,
                        ProbDist c)

Constructs a CircleIrradiator object

Parameters:

alpha - the average for the Poisson distribution used in the primary process

sec - a ProbDist object used used to determine how many points occur in the secondary process

c - a ProbDist object which represents the probability distribution used to position points found in the secondary process

Method Detail

irradiate

public void irradiate(java.util.Random rGen)
               throws java.lang.Exception

Description copied from class: Irradiator

Calling this method causes the irradiator class to generate a new array of Breaks in the Geometry set by setGeometry(). If no valid Geometry has been set, this method should throw an exception.

Specified by:

irradiate in class Irradiator

Throws:

java.lang.Exception

setGeometry

public void setGeometry(Geometry geo)
                 throws java.lang.Exception

Description copied from class: Irradiator

This method is intended to be used by the driver to specify the Geometry object which should be used as a basis for this irradiation process.

Specified by:

setGeometry in class Irradiator

Parameters:

geo - a Geometry object in which Breaks are to be found

Throws:

java.lang.Exception

breaks

public Break[] breaks()

Returns an array of the double strand breaks that occur during the course of the irradiation of the genome

Overrides:

breaks in class Irradiator

Returns:

an array of Break objects representing the breaks that occur during the course of the irradiation of the genome

sizeOfSecondary

public int sizeOfSecondary()

Returns the number of points in the secondary process

Returns:

an int of the number of points in the secondary process

sizeOfPrimary

public int sizeOfPrimary()

Returns the number of points in the primary process

Returns:

an int of the number of points in the primary process