com.objex.panywhere
Class ChromosomeMarker

java.lang.Object
  com.objex.panywhere.ChromosomeMarker

All Implemented Interfaces:

java.io.Serializable

public class ChromosomeMarker
extends java.lang.Object
implements java.io.Serializable

Class defines the Markers on a chromosome and the different Allele properties for each such Marker. A marker has two Alleles, one inherited from the mother and another inherited from the father.

Since:

Introduced version 1.01

See Also:

Serialized Form

Constructor Summary

ChromosomeMarker()
Creates a new Marker instance

Method Summary

ChromosomeMarker	cloneMarker() Creates and returns a new Marker object with the same properties as this Marker.
double	getGenetic_distance() Getter for property genetic_distance.
double	getLocation() Getter for property location.
Allele	getMaternalAllele() Getter for property maternalAllele.
java.lang.String	getName() Getter for property name.
Allele	getPaternalAllele() Getter for property parternalAllele.
int	getSequence() Getter for property sequence.
void	setGenetic_distance(double rhs) Setter for property genetic_distance.
void	setLocation(double rhs) Setter for property location.
void	setMaternalAllele(Allele rhs) Setter for property maternalAllele.
void	setName(java.lang.String rhs) Setter for property name.
void	setPaternalAllele(Allele rhs) Setter for property parternalAllele.
void	setSequence(int rhs) Setter for property sequence.

Methods inherited from class java.lang.Object

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

Constructor Detail

ChromosomeMarker

public ChromosomeMarker()

Creates a new Marker instance

Method Detail

getName

public java.lang.String getName()

Getter for property name.

Returns:

Value of property name.

setName

public void setName(java.lang.String rhs)

Setter for property name.

Parameters:

rhs - New value of property name.

getPaternalAllele

public Allele getPaternalAllele()

Getter for property parternalAllele.

Returns:

Value of property parternalAllele.

setPaternalAllele

public void setPaternalAllele(Allele rhs)

Setter for property parternalAllele.

Parameters:

rhs - New value of property parternalAllele.

getMaternalAllele

public Allele getMaternalAllele()

Getter for property maternalAllele.

Returns:

Value of property maternalAllele.

setMaternalAllele

public void setMaternalAllele(Allele rhs)

Setter for property maternalAllele.

Parameters:

rhs - New value of property maternalAllele.

getSequence

public int getSequence()

Getter for property sequence. The sequencing must be automatically determined depending on the location of the marker. The first marker on the chromosome will have a sequence of one(1)

Returns:

Value of property sequence.

setSequence

public void setSequence(int rhs)

Setter for property sequence. Getter for property sequence. The sequencing must be automatically determined depending on the location of the marker. The first marker on the chromosome will have a sequence of one(1)

Parameters:

rhs - New value of property sequence.

getGenetic_distance

public double getGenetic_distance()

Getter for property genetic_distance. Genetic distance refers to the gap (in centiMorgans cM) between this marker and the previous marker on the chromosome.

Returns:

Value of property genetic_distance.

setGenetic_distance

public void setGenetic_distance(double rhs)

Setter for property genetic_distance. Genetic distance refers to the gap (in centiMorgans cM) between this marker and the previous marker on the chromosome.

Parameters:

rhs - New value of property genetic_distance.

getLocation

public double getLocation()

Getter for property location. The location refers to the point on the chromosome on which this marker is located. It is measured in mBases. The location also determines the sequence of the marker.

Returns:

The current location of this marker on its parent chromosome

setLocation

public void setLocation(double rhs)

Setter for property location. The location refers to the point on the chromosome on which this marker is located. It is measured in mBases. The location also determines the sequence of the marker.

Parameters:

rhs - New value of property location.

cloneMarker

public ChromosomeMarker cloneMarker()

Creates and returns a new Marker object with the same properties as this Marker.

Returns:

a New ChromosomeMarker