com.objex.progeny.anywhere.data
Class MarkerData

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

All Implemented Interfaces:

java.io.Serializable

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

MarkerData contains a map of chromosomes that define the genetic data of a person.

See Also:

Chromosome, ChromosomeMarker, Serialized Form

Constructor Summary

MarkerData()
Creates a new instance of MarkerData

Method Summary

void	addChromosome(Chromosome a_chromosome) Add a new chromosome to the genetic data map
MarkerData	clone()
Chromosome	getChromosome(int ai_chromoid)
java.util.Map<java.lang.Integer,Chromosome>	getChromosomes()
ChromosomeMarker	getMarker(java.lang.String as_name)
java.util.Iterator<Chromosome>	iterator()
java.util.Iterator<ChromosomeMarker>	iterator(boolean ab_chromosome_order)
int	markersCount()
void	setChromosomes(java.util.Map<java.lang.Integer,Chromosome> a_chromosomes) Sets a new map of chromosomes keyed by chromosome ID.

Methods inherited from class java.lang.Object

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

Constructor Detail

MarkerData

public MarkerData()

Creates a new instance of MarkerData

Method Detail

setChromosomes

public void setChromosomes(java.util.Map<java.lang.Integer,Chromosome> a_chromosomes)

Sets a new map of chromosomes keyed by chromosome ID.

Parameters:

a_chromosomes - The new map of chromosomes keyed by chromosome ID.

getChromosomes

public java.util.Map<java.lang.Integer,Chromosome> getChromosomes()

Returns:

The current map of chromosomes keyed by chromosome ID.

getChromosome

public Chromosome getChromosome(int ai_chromoid)

Parameters:

ai_chromoid - The ID of the chromosome to be retrieved

Returns:

The chromosome with specified ID

addChromosome

public void addChromosome(Chromosome a_chromosome)

Add a new chromosome to the genetic data map

Parameters:

a_chromosome - The new chromosome

iterator

public java.util.Iterator<Chromosome> iterator()

Returns:

An iterator of chromosomes in chromosome sequence. The sequence is determined when the chromosomes are added to the genetic data map

markersCount

public int markersCount()

Returns:

Number of markers on all the chromosomes making up this genetic data object. If there are 10 chromosomes and each with 5 markers, then 50 will be returned.

getMarker

public ChromosomeMarker getMarker(java.lang.String as_name)

Parameters:

as_name - The name of the marker to be retrieved.

Returns:

The marker with the specified name or NULL if no such marker exists on any chromosome in the genetic data map

iterator

public java.util.Iterator<ChromosomeMarker> iterator(boolean ab_chromosome_order)

Parameters:

ab_chromosome_order - If true then markers will be returned in chromosome order and then by marker sequence within a chromosome. Otherwise the order will be marker sequence regardless of what chromosome the marker is on.

Returns:

An Iterator of all markers on all chromosomes on this marker set.

clone

public MarkerData clone()

Overrides:

clone in class java.lang.Object

Returns:

create a new GeneticData with same chromosomes and markers as this one