jebl.evolution.sequences
Class Nucleotides

java.lang.Object
  jebl.evolution.sequences.Nucleotides

public final class Nucleotides
extends Object

Author:

Andrew Rambaut, Alexei Drummond

Field Summary

static NucleotideState	A_STATE
static NucleotideState	B_STATE
static NucleotideState	C_STATE
static int	CANONICAL_STATE_COUNT
static NucleotideState[]	CANONICAL_STATES
static NucleotideState[]	COMPLEMENTARY_STATES
static NucleotideState	D_STATE
static NucleotideState	G_STATE
static NucleotideState	GAP_STATE
static NucleotideState	H_STATE
static NucleotideState	K_STATE
static NucleotideState	M_STATE
static NucleotideState	N_STATE
static String	NAME
static NucleotideState	R_STATE
static NucleotideState	S_STATE
static int	STATE_COUNT
static NucleotideState[]	STATES
static NucleotideState	T_STATE
static NucleotideState	U_STATE
static NucleotideState	UNKNOWN_STATE
static NucleotideState	V_STATE
static NucleotideState	W_STATE
static NucleotideState	Y_STATE

Constructor Summary

Nucleotides()

Method Summary

static int	getCanonicalStateCount()
static List<NucleotideState>	getCanonicalStates()
static NucleotideState	getGapState()
String	getName()
static NucleotideState	getState(char code)
static NucleotideState	getState(int index)
static NucleotideState	getState(String code)
static int	getStateCount()
static List<State>	getStates()
static NucleotideState	getUnknownState()
static boolean	isATstate(State state)
static boolean	isGap(NucleotideState state)
static boolean	isGCstate(State state)
static boolean	isPurine(State state)
static boolean	isPyrimidine(State state)
static boolean	isTransition(State state1, State state2)
static boolean	isTransversion(State state1, State state2)
static boolean	isUnknown(NucleotideState state)
static NucleotideState[]	toStateArray(byte[] indexArray)
static NucleotideState[]	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

A_STATE

public static final NucleotideState A_STATE

C_STATE

public static final NucleotideState C_STATE

G_STATE

public static final NucleotideState G_STATE

T_STATE

public static final NucleotideState T_STATE

U_STATE

public static final NucleotideState U_STATE

R_STATE

public static final NucleotideState R_STATE

Y_STATE

public static final NucleotideState Y_STATE

M_STATE

public static final NucleotideState M_STATE

W_STATE

public static final NucleotideState W_STATE

S_STATE

public static final NucleotideState S_STATE

K_STATE

public static final NucleotideState K_STATE

B_STATE

public static final NucleotideState B_STATE

D_STATE

public static final NucleotideState D_STATE

H_STATE

public static final NucleotideState H_STATE

V_STATE

public static final NucleotideState V_STATE

N_STATE

public static final NucleotideState N_STATE

UNKNOWN_STATE

public static final NucleotideState UNKNOWN_STATE

GAP_STATE

public static final NucleotideState GAP_STATE

CANONICAL_STATES

public static final NucleotideState[] CANONICAL_STATES

STATES

public static final NucleotideState[] STATES

COMPLEMENTARY_STATES

public static final NucleotideState[] COMPLEMENTARY_STATES

Constructor Detail

Nucleotides

public Nucleotides()

Method Detail

getStateCount

public static int getStateCount()

getStates

public static List<State> getStates()

getCanonicalStateCount

public static int getCanonicalStateCount()

getCanonicalStates

public static List<NucleotideState> getCanonicalStates()

getState

public static NucleotideState getState(char code)

getState

public static NucleotideState getState(String code)

getState

public static NucleotideState getState(int index)

getUnknownState

public static NucleotideState getUnknownState()

getGapState

public static NucleotideState getGapState()

isUnknown

public static boolean isUnknown(NucleotideState state)

isGap

public static boolean isGap(NucleotideState state)

isTransition

public static boolean isTransition(State state1,
                                   State state2)

isTransversion

public static boolean isTransversion(State state1,
                                     State state2)

isPurine

public static boolean isPurine(State state)

isPyrimidine

public static boolean isPyrimidine(State state)

isGCstate

public static boolean isGCstate(State state)

isATstate

public static boolean isATstate(State state)

getName

public String getName()

toStateArray

public static NucleotideState[] toStateArray(String sequenceString)

toStateArray

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