com.objex.progeny.anywhere.data
Class ChromosomeMarker

java.lang.Object
  com.objex.progeny.anywhere.data.ChromosomeMarker

All Implemented Interfaces:

java.io.Serializable

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

Defines a marker within a chromosome. A marker has two alleles, the paternal allele and the marternal allele.

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.
java.lang.String	getAlias()
double	getBasePairs()
double	getCM()
double	getGenetic_distance() Getter for property genetic_distance.
double	getLocation() Getter for property location.
Allele	getMaternalAllele()
java.lang.String	getName() Getter for property name.
Allele	getPaternalAllele()
int	getSequence() Getter for property sequence.
void	setAlias(java.lang.String alias) Sets a new alias for the marker
void	setBasePairs(double basePairs) Set the genetic distance for this marker base pairs
void	setCM(double cM) Set the genetic distance for this marker cM
void	setGenetic_distance(double rhs) Setter for property genetic_distance.
void	setLocation(double rhs) Setter for property location.
void	setMaternalAllele(Allele rhs) Set the maternal allele to specified value
void	setName(java.lang.String rhs) Setter for property name.
void	setPaternalAllele(Allele rhs) Set the parternal allele.
void	setSequence(int rhs) Setter for property sequence.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, 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.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

setName

public void setName(java.lang.String rhs)

Setter for property name.

Parameters:

rhs - New value of property name.

getPaternalAllele

public Allele getPaternalAllele()

Returns:

The paternal allele

setPaternalAllele

public void setPaternalAllele(Allele rhs)

Set the parternal allele.

Parameters:

rhs - The new parternal allele.

getMaternalAllele

public Allele getMaternalAllele()

Returns:

The maternal allele

setMaternalAllele

public void setMaternalAllele(Allele rhs)

Set the maternal allele to specified value

Parameters:

rhs - The new maternal allele

getSequence

public int getSequence()

Getter for property sequence. The sequencing must be automatically determined depending on the location of the marker on the haplotype in question. So if you have a hpalotype with 10 markes and marker rs200 is on position 10 then the seuqnec is 1.

**NOTE** This seuqnece is within the haplotype of which this marker is part and not within the chromosome

Returns:

Value of property sequence.

setSequence

public void setSequence(int rhs)

Setter for property sequence. The sequencing must be automatically determined depending on the location of the marker on the haplotype in question. So if you have a hpalotype with 10 markes and marker rs200 is on position 10 then the sequence for this marker is 10.

**NOTE** This seuqnece is within the haplotype of which this marker is part and not within the chromosome *

Sequence must be set only if it is unset i.e. if getSequence return -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

getAlias

public java.lang.String getAlias()

Returns:

The alias for this marker

setAlias

public void setAlias(java.lang.String alias)

Sets a new alias for the marker

Parameters:

alias - The new alias to set

getCM

public double getCM()

Returns:

The genetic distance in cM

setCM

public void setCM(double cM)

Set the genetic distance for this marker cM

Parameters:

cM - The genetic distance in cM

getBasePairs

public double getBasePairs()

Returns:

The genetic distance in basePairs

setBasePairs

public void setBasePairs(double basePairs)

Set the genetic distance for this marker base pairs

Parameters:

basePairs - The genetic distance in bP