org.jscience.biology
Class Alphabet

java.lang.Object
  extended by org.jscience.biology.Alphabet
All Implemented Interfaces:
Named

public class Alphabet
extends java.lang.Object
implements Named

An class used to define the process by which mRNA is transformed (:translation) into a protein according to a given code.


Constructor Summary
Alphabet(java.lang.String name, java.lang.String aminoAcids, java.lang.String startCodons)
          Creates a new Alphabet object.
 
Method Summary
 boolean equals(java.lang.Object o)
          DOCUMENT ME!
 AminoAcid getAminoAcid(Base base1, Base base2, Base base3)
          DOCUMENT ME!
 java.lang.String getAminoAcids()
          DOCUMENT ME!
 java.util.Set getInitiationCodons()
          DOCUMENT ME!
 java.lang.String getName()
          DOCUMENT ME!
 java.lang.String getStartCodons()
          DOCUMENT ME!
 java.util.Set getTerminationCodons()
          DOCUMENT ME!
 boolean isStartCodon(Base base1, Base base2, Base base3)
          DOCUMENT ME!
 boolean isStopCodon(Base base1, Base base2, Base base3)
          DOCUMENT ME!
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Alphabet

public Alphabet(java.lang.String name,
                java.lang.String aminoAcids,
                java.lang.String startCodons)
Creates a new Alphabet object.

Parameters:
name - DOCUMENT ME!
aminoAcids - DOCUMENT ME!
startCodons - DOCUMENT ME!
Throws:
java.lang.IllegalArgumentException - DOCUMENT ME!
Method Detail

getName

public java.lang.String getName()
DOCUMENT ME!

Specified by:
getName in interface Named
Returns:
DOCUMENT ME!

getAminoAcids

public java.lang.String getAminoAcids()
DOCUMENT ME!

Returns:
DOCUMENT ME!

getStartCodons

public java.lang.String getStartCodons()
DOCUMENT ME!

Returns:
DOCUMENT ME!

isStartCodon

public boolean isStartCodon(Base base1,
                            Base base2,
                            Base base3)
DOCUMENT ME!

Parameters:
base1 - DOCUMENT ME!
base2 - DOCUMENT ME!
base3 - DOCUMENT ME!
Returns:
DOCUMENT ME!
Throws:
java.lang.IllegalArgumentException - DOCUMENT ME!

getInitiationCodons

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

Returns:
DOCUMENT ME!

getAminoAcid

public AminoAcid getAminoAcid(Base base1,
                              Base base2,
                              Base base3)
DOCUMENT ME!

Parameters:
base1 - DOCUMENT ME!
base2 - DOCUMENT ME!
base3 - DOCUMENT ME!
Returns:
DOCUMENT ME!

isStopCodon

public boolean isStopCodon(Base base1,
                           Base base2,
                           Base base3)
DOCUMENT ME!

Parameters:
base1 - DOCUMENT ME!
base2 - DOCUMENT ME!
base3 - DOCUMENT ME!
Returns:
DOCUMENT ME!
Throws:
java.lang.IllegalArgumentException - DOCUMENT ME!

getTerminationCodons

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

Returns:
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!