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