Package ca.cas.montecarlo

Provides classes which simulate various stages in the process of forming chromosome aberrations.

See:
Description

Class Summary

Break	Each Break object represents a double strand break on a Chromosome object
CircleGeometry	Each CircleGeometry object represents the relative positioning of chromosomes from a particular genome as arranged in a circle.
CircleIrradiator	Each CircleIrradiator object represents the process in which a genome arranged as a CircleGeometry is irradiated and double strand breaks occur.
ExponentialMisrejoiner	ExponentialMisrejoiner extends Misrejoiner with the rule that the probability of two free ends joining decays exponentially with the distance between the two free ends in the Geometry
Geometry	A class that extends Geometry represents the spatial relationship of the Chromosomes in a Genome.
Irradiator	A class that extends Irradiator represents the process in which double strand breaks are induced in a genome by ionizing radiation.
Misrejoiner	A class that extends Misrejoiner represents the process of rejoining the loose ends that are the result of the irradiation of a genome.

Package ca.cas.montecarlo Description

Provides classes which simulate various stages in the process of forming chromosome aberrations. Many of these classes are randomized using the Java class Random. The three main types of classes in this package are Geometries, Irradiators, and Misrejoiners. Each general type has an abstract class associated with it. These abstract classes contain methods and fields common to all classes of each type. They also establish a manner in which extending classes of each type are to be written. The design of the classes in the ca.cas.control package relies on the fact that classes of the three general types extend the appropriate abstract class.