jebl.evolution.sequences
Class Codons

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

public final class Codons
extends Object

Author:

Andrew Rambaut, Alexei Drummond

Field Summary

static int	CANONICAL_STATE_COUNT
static CodonState[]	CANONICAL_STATES
static CodonState	GAP_STATE
static String	NAME
static int	STATE_COUNT
static CodonState[]	STATES
static CodonState	UNKNOWN_STATE

Constructor Summary

Codons()

Method Summary

static int	getCanonicalStateCount()
static List<State>	getCanonicalStates()
static CodonState	getGapState()
static CodonState	getState(int index)
static CodonState	getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
static CodonState	getState(String code) Gets the state object for the given code.
static int	getStateCount()
static 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(String sequenceString)

Methods inherited from class java.lang.Object

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

Field Detail

NAME

public static final 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 List<State> getStates()

getCanonicalStateCount

public static int getCanonicalStateCount()

getCanonicalStates

public static List<State> getCanonicalStates()

getState

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

getState

public static CodonState getState(String code)

Gets the state object for the given code. Returns null if the code is illegal.

Parameters:

code - a three-character string of 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(String sequenceString)

toStateArray

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