jebl.evolution.sequences
Class AminoAcids

java.lang.Object
  jebl.evolution.sequences.AminoAcids

public final class AminoAcids
extends Object

Author:

Andrew Rambaut, Alexei Drummond

Field Summary

static AminoAcidState	A_STATE
static AminoAcidState	B_STATE
static AminoAcidState	C_STATE
static int	CANONICAL_STATE_COUNT
static AminoAcidState[]	CANONICAL_STATES
static StateClassification	CHEMICAL_CLASSIFICATION
static AminoAcidState	D_STATE
static AminoAcidState	E_STATE
static AminoAcidState	F_STATE
static AminoAcidState	G_STATE
static AminoAcidState	GAP_STATE
static AminoAcidState	H_STATE
static StateClassification	HYDROPATHY_CLASSIFICATION
static AminoAcidState	I_STATE
static AminoAcidState	K_STATE
static AminoAcidState	L_STATE
static AminoAcidState	M_STATE
static AminoAcidState	N_STATE
static String	NAME
static AminoAcidState	P_STATE
static AminoAcidState	Q_STATE
static AminoAcidState	R_STATE
static AminoAcidState	S_STATE
static int	STATE_COUNT
static AminoAcidState[]	STATES
static AminoAcidState	STOP_STATE
static AminoAcidState	T_STATE
static AminoAcidState	UNKNOWN_STATE
static AminoAcidState	V_STATE
static StateClassification	VOLUME_CLASSIFICATION
static AminoAcidState	W_STATE
static AminoAcidState	X_STATE
static AminoAcidState	Y_STATE
static AminoAcidState	Z_STATE

Constructor Summary

AminoAcids()

Method Summary

static int	getCanonicalStateCount()
static List<State>	getCanonicalStates()
static AminoAcidState	getGapState()
static AminoAcidState	getState(char code)
static AminoAcidState	getState(int index)
static AminoAcidState	getState(String code)
static int	getStateCount()
static List<AminoAcidState>	getStates()
static String	getTripletCode(AminoAcidState state)
static AminoAcidState	getUnknownState()
static boolean	isGap(AminoAcidState state)
static boolean	isUnknown(AminoAcidState state)
static AminoAcidState[]	toStateArray(byte[] indexArray)
static AminoAcidState[]	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 AminoAcidState A_STATE

C_STATE

public static final AminoAcidState C_STATE

D_STATE

public static final AminoAcidState D_STATE

E_STATE

public static final AminoAcidState E_STATE

F_STATE

public static final AminoAcidState F_STATE

G_STATE

public static final AminoAcidState G_STATE

H_STATE

public static final AminoAcidState H_STATE

I_STATE

public static final AminoAcidState I_STATE

K_STATE

public static final AminoAcidState K_STATE

L_STATE

public static final AminoAcidState L_STATE

M_STATE

public static final AminoAcidState M_STATE

N_STATE

public static final AminoAcidState N_STATE

P_STATE

public static final AminoAcidState P_STATE

Q_STATE

public static final AminoAcidState Q_STATE

R_STATE

public static final AminoAcidState R_STATE

S_STATE

public static final AminoAcidState S_STATE

T_STATE

public static final AminoAcidState T_STATE

V_STATE

public static final AminoAcidState V_STATE

W_STATE

public static final AminoAcidState W_STATE

Y_STATE

public static final AminoAcidState Y_STATE

CANONICAL_STATES

public static final AminoAcidState[] CANONICAL_STATES

B_STATE

public static final AminoAcidState B_STATE

Z_STATE

public static final AminoAcidState Z_STATE

X_STATE

public static final AminoAcidState X_STATE

UNKNOWN_STATE

public static final AminoAcidState UNKNOWN_STATE

STOP_STATE

public static final AminoAcidState STOP_STATE

GAP_STATE

public static final AminoAcidState GAP_STATE

STATES

public static final AminoAcidState[] STATES

CHEMICAL_CLASSIFICATION

public static final StateClassification CHEMICAL_CLASSIFICATION

HYDROPATHY_CLASSIFICATION

public static final StateClassification HYDROPATHY_CLASSIFICATION

VOLUME_CLASSIFICATION

public static final StateClassification VOLUME_CLASSIFICATION

Constructor Detail

AminoAcids

public AminoAcids()

Method Detail

getStateCount

public static int getStateCount()

getStates

public static List<AminoAcidState> getStates()

getCanonicalStateCount

public static int getCanonicalStateCount()

getCanonicalStates

public static List<State> getCanonicalStates()

getState

public static AminoAcidState getState(char code)

getState

public static AminoAcidState getState(String code)

getState

public static AminoAcidState getState(int index)

getUnknownState

public static AminoAcidState getUnknownState()

getGapState

public static AminoAcidState getGapState()

isUnknown

public static boolean isUnknown(AminoAcidState state)

isGap

public static boolean isGap(AminoAcidState state)

getTripletCode

public static String getTripletCode(AminoAcidState state)

toStateArray

public static AminoAcidState[] toStateArray(String sequenceString)

toStateArray

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