java.lang.Object

jebl.evolution.sequences.AminoAcids

public final class AminoAcids extends Object

Uninstantiable utility class with only static methods.

Version:: $Id: AminoAcids.java 986 2009-03-10 01:00:03Z matt_kearse $
Author:: Andrew Rambaut, Alexei Drummond

Field Summary

Fields

Modifier and Type

Field

Description

static final AminoAcidState

A_STATE

static final AminoAcidState

B_STATE

static final AminoAcidState

C_STATE

static final int

CANONICAL_STATE_COUNT

static final AminoAcidState[]

CANONICAL_STATES

Deprecated.

static final StateClassification

CHEMICAL_CLASSIFICATION

static final AminoAcidState

D_STATE

static final AminoAcidState

E_STATE

static final AminoAcidState

F_STATE

static final AminoAcidState

G_STATE

static final AminoAcidState

GAP_STATE

static final AminoAcidState

H_STATE

static final StateClassification

HYDROPATHY_CLASSIFICATION

static final AminoAcidState

I_STATE

static final AminoAcidState

J_STATE

static final AminoAcidState

K_STATE

static final AminoAcidState

L_STATE

static final AminoAcidState

M_STATE

static final AminoAcidState

N_STATE

static final String

NAME

static final AminoAcidState

O_STATE

static final AminoAcidState

P_STATE

static final AminoAcidState

Q_STATE

static final AminoAcidState

R_STATE

static final AminoAcidState

S_STATE

static final int

STATE_COUNT

static final AminoAcidState[]

STATES

Deprecated.

static final AminoAcidState

STOP_STATE

static final AminoAcidState

T_STATE

static final AminoAcidState

U_STATE

static final AminoAcidState

UNKNOWN_STATE

static final AminoAcidState

V_STATE

static final StateClassification

VOLUME_CLASSIFICATION

static final AminoAcidState

W_STATE

static final AminoAcidState

X_STATE

static final AminoAcidState

Y_STATE

static final AminoAcidState

Z_STATE
Method Summary

Modifier and Type

Method

Description

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

Field Details
- 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
- U_STATE
  
  public static final AminoAcidState U_STATE
- O_STATE
  
  public static final AminoAcidState O_STATE
- CANONICAL_STATES
  
  @Deprecated public static final AminoAcidState[] CANONICAL_STATES
  
  Deprecated.
- B_STATE
  
  public static final AminoAcidState B_STATE
- Z_STATE
  
  public static final AminoAcidState Z_STATE
- J_STATE
  
  public static final AminoAcidState J_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
  
  @Deprecated public static final AminoAcidState[] STATES
  
  Deprecated.
- CHEMICAL_CLASSIFICATION
  
  public static final StateClassification CHEMICAL_CLASSIFICATION
- HYDROPATHY_CLASSIFICATION
  
  public static final StateClassification HYDROPATHY_CLASSIFICATION
- VOLUME_CLASSIFICATION
  
  public static final StateClassification VOLUME_CLASSIFICATION
Method Details
- 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)

Class AminoAcids

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

NAME

CANONICAL_STATE_COUNT

STATE_COUNT

A_STATE

C_STATE

D_STATE

E_STATE

F_STATE

G_STATE

H_STATE

I_STATE

K_STATE

L_STATE

M_STATE

N_STATE

P_STATE

Q_STATE

R_STATE

S_STATE

T_STATE

V_STATE

W_STATE

Y_STATE

U_STATE

O_STATE

CANONICAL_STATES

B_STATE

Z_STATE

J_STATE

X_STATE

UNKNOWN_STATE

STOP_STATE

GAP_STATE

STATES

CHEMICAL_CLASSIFICATION

HYDROPATHY_CLASSIFICATION

VOLUME_CLASSIFICATION

Method Details

getStateCount

getStates

getCanonicalStateCount

getCanonicalStates

getState

getState

getState

getUnknownState

getGapState

isUnknown

isGap

getTripletCode

toStateArray

toStateArray