org.jscience.biology
Class DNA

java.lang.Object
  extended by org.jscience.biology.Chain
      extended by org.jscience.biology.DNA
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable

public class DNA
extends Chain
implements java.io.Serializable, java.lang.Cloneable

A class representing a DNA strain and accounting for chromosome information (the histones are missing).

See Also:
Serialized Form

Constructor Summary
DNA(Base[] bases)
          Constructs a DNA representation.
 
Method Summary
 java.lang.Object clone()
          DOCUMENT ME!
 Base[] getBases()
          DOCUMENT ME!
 Chain getComplementary()
          Returns a complementary strain deduced from this one.
 Base getComplementary(Base base)
          DOCUMENT ME!
 int getLength()
          DOCUMENT ME!
 java.util.Set getValidBases()
          DOCUMENT ME!
 
Methods inherited from class org.jscience.biology.Chain
equals
 
Methods inherited from class java.lang.Object
finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

DNA

public DNA(Base[] bases)
Constructs a DNA representation. The array of base should not contain the Uracil base. Only one of the two strains is coded, the complementary strain is deduced from this one.

Parameters:
bases - DOCUMENT ME!
Throws:
java.lang.IllegalArgumentException - DOCUMENT ME!
Method Detail

getBases

public Base[] getBases()
DOCUMENT ME!

Specified by:
getBases in class Chain
Returns:
DOCUMENT ME!

getLength

public int getLength()
DOCUMENT ME!

Specified by:
getLength in class Chain
Returns:
DOCUMENT ME!

getComplementary

public Base getComplementary(Base base)
DOCUMENT ME!

Specified by:
getComplementary in class Chain
Parameters:
base - DOCUMENT ME!
Returns:
DOCUMENT ME!

getComplementary

public Chain getComplementary()
Returns a complementary strain deduced from this one.

Specified by:
getComplementary in class Chain
Returns:
DOCUMENT ME!

getValidBases

public java.util.Set getValidBases()
DOCUMENT ME!

Specified by:
getValidBases in class Chain
Returns:
DOCUMENT ME!

clone

public java.lang.Object clone()
DOCUMENT ME!

Specified by:
clone in class Chain
Returns:
DOCUMENT ME!