Package jebl.evolution.sequences
Class AminoAcids
- java.lang.Object
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- jebl.evolution.sequences.AminoAcids
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public final class AminoAcids extends java.lang.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
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Field Summary
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static int
getCanonicalStateCount()
static java.util.List<State>
getCanonicalStates()
static AminoAcidState
getGapState()
static AminoAcidState
getState(char code)
static AminoAcidState
getState(int index)
static AminoAcidState
getState(java.lang.String code)
static int
getStateCount()
static java.util.List<AminoAcidState>
getStates()
static java.lang.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(java.lang.String sequenceString)
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Field Detail
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NAME
public static final java.lang.String NAME
- See Also:
- Constant Field Values
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CANONICAL_STATE_COUNT
public static final int CANONICAL_STATE_COUNT
- See Also:
- Constant Field Values
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STATE_COUNT
public static final int STATE_COUNT
- See Also:
- Constant Field Values
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A_STATE
public static final AminoAcidState A_STATE
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C_STATE
public static final AminoAcidState C_STATE
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D_STATE
public static final AminoAcidState D_STATE
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E_STATE
public static final AminoAcidState E_STATE
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F_STATE
public static final AminoAcidState F_STATE
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G_STATE
public static final AminoAcidState G_STATE
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H_STATE
public static final AminoAcidState H_STATE
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I_STATE
public static final AminoAcidState I_STATE
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K_STATE
public static final AminoAcidState K_STATE
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L_STATE
public static final AminoAcidState L_STATE
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M_STATE
public static final AminoAcidState M_STATE
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N_STATE
public static final AminoAcidState N_STATE
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P_STATE
public static final AminoAcidState P_STATE
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Q_STATE
public static final AminoAcidState Q_STATE
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R_STATE
public static final AminoAcidState R_STATE
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S_STATE
public static final AminoAcidState S_STATE
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T_STATE
public static final AminoAcidState T_STATE
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V_STATE
public static final AminoAcidState V_STATE
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W_STATE
public static final AminoAcidState W_STATE
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Y_STATE
public static final AminoAcidState Y_STATE
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U_STATE
public static final AminoAcidState U_STATE
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O_STATE
public static final AminoAcidState O_STATE
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CANONICAL_STATES
@Deprecated public static final AminoAcidState[] CANONICAL_STATES
Deprecated.
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B_STATE
public static final AminoAcidState B_STATE
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Z_STATE
public static final AminoAcidState Z_STATE
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J_STATE
public static final AminoAcidState J_STATE
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X_STATE
public static final AminoAcidState X_STATE
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UNKNOWN_STATE
public static final AminoAcidState UNKNOWN_STATE
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STOP_STATE
public static final AminoAcidState STOP_STATE
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GAP_STATE
public static final AminoAcidState GAP_STATE
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STATES
@Deprecated public static final AminoAcidState[] STATES
Deprecated.
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CHEMICAL_CLASSIFICATION
public static final StateClassification CHEMICAL_CLASSIFICATION
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HYDROPATHY_CLASSIFICATION
public static final StateClassification HYDROPATHY_CLASSIFICATION
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VOLUME_CLASSIFICATION
public static final StateClassification VOLUME_CLASSIFICATION
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Method Detail
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getStateCount
public static int getStateCount()
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getStates
public static java.util.List<AminoAcidState> getStates()
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getCanonicalStateCount
public static int getCanonicalStateCount()
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getCanonicalStates
public static java.util.List<State> getCanonicalStates()
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getState
public static AminoAcidState getState(char code)
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getState
public static AminoAcidState getState(java.lang.String code)
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getState
public static AminoAcidState getState(int index)
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getUnknownState
public static AminoAcidState getUnknownState()
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getGapState
public static AminoAcidState getGapState()
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isUnknown
public static boolean isUnknown(AminoAcidState state)
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isGap
public static boolean isGap(AminoAcidState state)
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getTripletCode
public static java.lang.String getTripletCode(AminoAcidState state)
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toStateArray
public static AminoAcidState[] toStateArray(java.lang.String sequenceString)
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toStateArray
public static AminoAcidState[] toStateArray(byte[] indexArray)
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