jebl.evolution.sequences
Class Codons

java.lang.Object
  extended by jebl.evolution.sequences.Codons

public final class Codons
extends java.lang.Object

Version:
$Id: Codons.java 744 2007-07-30 02:57:11Z twobeers $
Author:
Andrew Rambaut, Alexei Drummond

Field Summary
static int CANONICAL_STATE_COUNT
           
static CodonState[] CANONICAL_STATES
           
static CodonState GAP_STATE
           
static java.lang.String NAME
           
static int STATE_COUNT
           
static CodonState[] STATES
           
static CodonState UNKNOWN_STATE
           
 
Constructor Summary
Codons()
           
 
Method Summary
static int getCanonicalStateCount()
           
static java.util.List<State> getCanonicalStates()
           
static CodonState getGapState()
           
static CodonState getState(int index)
           
static CodonState getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
           
static CodonState getState(java.lang.String code)
          Gets the state object for the given code.
static int getStateCount()
           
static java.util.List<State> getStates()
           
static CodonState getUnknownState()
           
static boolean isGap(CodonState state)
           
static boolean isUnknown(CodonState state)
           
static NucleotideState[] toNucleotides(CodonState state)
           
static CodonState[] toStateArray(byte[] indexArray)
           
static CodonState[] toStateArray(java.lang.String sequenceString)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

NAME

public static final java.lang.String NAME
See Also:
Constant Field Values

CANONICAL_STATE_COUNT

public static final int CANONICAL_STATE_COUNT
See Also:
Constant Field Values

STATE_COUNT

public static final int STATE_COUNT
See Also:
Constant Field Values

CANONICAL_STATES

public static final CodonState[] CANONICAL_STATES

STATES

public static final CodonState[] STATES

UNKNOWN_STATE

public static final CodonState UNKNOWN_STATE

GAP_STATE

public static final CodonState GAP_STATE
Constructor Detail

Codons

public Codons()
Method Detail

getStateCount

public static int getStateCount()

getStates

public static java.util.List<State> getStates()

getCanonicalStateCount

public static int getCanonicalStateCount()

getCanonicalStates

public static java.util.List<State> getCanonicalStates()

getState

public static CodonState getState(NucleotideState nucleotide1,
                                  NucleotideState nucleotide2,
                                  NucleotideState nucleotide3)

getState

public static CodonState getState(java.lang.String code)
Gets the state object for the given code. Returns null if the code is illegal or contains ambiguous nucleotides.

Parameters:
code - a three-character string of non-ambiguous nucleotides in uppercase
Returns:
the state

getState

public static CodonState getState(int index)

getUnknownState

public static CodonState getUnknownState()

getGapState

public static CodonState getGapState()

isUnknown

public static boolean isUnknown(CodonState state)

isGap

public static boolean isGap(CodonState state)

toNucleotides

public static NucleotideState[] toNucleotides(CodonState state)

toStateArray

public static CodonState[] toStateArray(java.lang.String sequenceString)

toStateArray

public static CodonState[] toStateArray(byte[] indexArray)


http://code.google.com/p/jebl2/