org.jscience.biology
Class Genome

java.lang.Object
  extended by 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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See Also:
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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See Also:
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:
DOCUMENT ME!

getKind

public int getKind()
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Returns:
DOCUMENT ME!

setKind

public void setKind(int kind)
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Parameters:
kind - DOCUMENT ME!

equals

public boolean equals(java.lang.Object o)
DOCUMENT ME!

Overrides:
equals in class java.lang.Object
Parameters:
o - DOCUMENT ME!
Returns:
DOCUMENT ME!