public final class Codons
extends java.lang.Object
Modifier and Type | Field and 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 |
Constructor and Description |
---|
Codons() |
Modifier and Type | Method and Description |
---|---|
static int |
getCanonicalStateCount() |
static java.util.List<State> |
getCanonicalStates() |
static CodonState |
getGapState() |
static CodonState |
getState(int index) |
static CodonState |
getState(NucleotideState nucleotide1,
NucleotideState nucleotide2,
NucleotideState nucleotide3) |
static CodonState |
getState(java.lang.String code)
Gets the state object for the given code.
|
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 CodonState[] |
toStateArray(byte[] indexArray) |
static CodonState[] |
toStateArray(java.lang.String sequenceString) |
public static final java.lang.String NAME
public static final int CANONICAL_STATE_COUNT
public static final int STATE_COUNT
public static final CodonState[] CANONICAL_STATES
public static final CodonState[] STATES
public static final CodonState UNKNOWN_STATE
public static final CodonState GAP_STATE
public static int getStateCount()
public static java.util.List<State> getStates()
public static int getCanonicalStateCount()
public static java.util.List<State> getCanonicalStates()
public static CodonState getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
public static CodonState getState(java.lang.String code)
code
- a three-character string of non-ambiguous nucleotides in uppercasepublic static CodonState getState(int index)
public static CodonState getUnknownState()
public static CodonState getGapState()
public static boolean isUnknown(CodonState state)
public static boolean isGap(CodonState state)
public static NucleotideState[] toNucleotides(CodonState state)
public static CodonState[] toStateArray(java.lang.String sequenceString)
public static CodonState[] toStateArray(byte[] indexArray)
http://code.google.com/p/jebl2/