org.jscience.biology
Class Genome

java.lang.Object
  org.jscience.biology.Genome

public class Genome
extends java.lang.Object

A class representing the whole genome of an individual. For example see ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ for the canonical human genome sequence

Field Summary

static int	ANEUPLOID DOCUMENT ME!
static int	DIPLOID DOCUMENT ME!
static int	HAPLOID DOCUMENT ME!
static int	POLYPLOID DOCUMENT ME!
static int	UNKNOWN DOCUMENT ME!

Constructor Summary

Genome(Chain[] chains)
Constructs a genome.

Method Summary

boolean	equals(java.lang.Object o) DOCUMENT ME!
Chain[]	getChains() DOCUMENT ME!
int	getKind() DOCUMENT ME!
void	setKind(int kind) DOCUMENT ME!

Methods inherited from class java.lang.Object

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

Field Detail

UNKNOWN

public static final int UNKNOWN

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See Also:

Constant Field Values

HAPLOID

public static final int HAPLOID

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Constant Field Values

DIPLOID

public static final int DIPLOID

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See Also:

Constant Field Values

POLYPLOID

public static final int POLYPLOID

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Constant Field Values

ANEUPLOID

public static final int ANEUPLOID

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See Also:

Constant Field Values

Constructor Detail

Genome

public Genome(Chain[] chains)

Constructs a genome. For diploid (or higher) genomes (which length should be dividable by two), please get sure that the second half of the array contains the homologous genes in the same order than the first half, as this information is used in cell meiosis.

Parameters:

chains - DOCUMENT ME!

Throws:

java.lang.IllegalArgumentException - DOCUMENT ME!

Method Detail

getChains

public Chain[] getChains()

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Returns:

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getKind

public int getKind()

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Returns:

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setKind

public void setKind(int kind)

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Parameters:

kind - DOCUMENT ME!

equals

public boolean equals(java.lang.Object o)

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Overrides:

equals in class java.lang.Object

Parameters:

o - DOCUMENT ME!

Returns:

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