Package jebl.evolution.sequences
Class Codons
- java.lang.Object
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- jebl.evolution.sequences.Codons
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public final class Codons extends java.lang.Object
- Version:
- $Id: Codons.java 744 2007-07-30 02:57:11Z twobeers $
- Author:
- Andrew Rambaut, Alexei Drummond
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Field Summary
Fields Modifier and Type Field Description static int
CANONICAL_STATE_COUNT
static CodonState[]
CANONICAL_STATES
static CodonState
GAP_STATE
static java.lang.String
NAME
static int
STATE_COUNT
static CodonState[]
STATES
static CodonState
UNKNOWN_STATE
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Constructor Summary
Constructors Constructor Description Codons()
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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 CodonState
getGapState()
static CodonState
getState(int index)
static CodonState
getState(java.lang.String code)
Gets the state object for the given code.static CodonState
getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
static int
getStateCount()
static java.util.List<State>
getStates()
static CodonState
getUnknownState()
static boolean
isGap(CodonState state)
static boolean
isUnknown(CodonState state)
static NucleotideState[]
toNucleotides(CodonState state)
static NucleotideState[]
toNucleotides(State[] states)
static CodonState[]
toStateArray(byte[] indexArray)
static CodonState[]
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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CANONICAL_STATES
public static final CodonState[] CANONICAL_STATES
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STATES
public static final CodonState[] STATES
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UNKNOWN_STATE
public static final CodonState UNKNOWN_STATE
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GAP_STATE
public static final CodonState GAP_STATE
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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<State> 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 CodonState getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
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getState
public static CodonState getState(java.lang.String code)
Gets the state object for the given code. Returns null if the code is illegal or contains ambiguous nucleotides.- Parameters:
code
- a three-character string of non-ambiguous nucleotides in uppercase- Returns:
- the state
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getState
public static CodonState getState(int index)
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getUnknownState
public static CodonState getUnknownState()
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getGapState
public static CodonState getGapState()
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isUnknown
public static boolean isUnknown(CodonState state)
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isGap
public static boolean isGap(CodonState state)
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toNucleotides
public static NucleotideState[] toNucleotides(State[] states)
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toNucleotides
public static NucleotideState[] toNucleotides(CodonState state)
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toStateArray
public static CodonState[] toStateArray(java.lang.String sequenceString)
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toStateArray
public static CodonState[] toStateArray(byte[] indexArray)
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