public final class AminoAcidAlphabet extends Alphabet<S>
"_" represents incomplete codon (residual 1 or 2 nucleotides remaining after translation of all full codons)
Alphabet,
AminoAcidSequence,
Sequence,
Serialized FormAlphabet.AlphabetSerialization| Modifier and Type | Field and Description |
|---|---|
static byte |
A
Alanine byte representation
|
static Wildcard |
A_WILDCARD
Alanine wildcard
|
static byte |
B
Aspartic acid or Asparagine (N or D) byte representation
|
static Wildcard |
B_WILDCARD
Aspartic acid or Asparagine (N or D) wildcard
|
static byte |
C
Cysteine byte representation
|
static Wildcard |
C_WILDCARD
Cysteine wildcard
|
static byte |
D
Aspartic Acid byte representation
|
static Wildcard |
D_WILDCARD
Aspartic Acid wildcard
|
static byte |
E
Glutamic Acid representation
|
static Wildcard |
E_WILDCARD
Glutamic Acid wildcard
|
static byte |
F
Phenylalanine byte representation
|
static Wildcard |
F_WILDCARD
Phenylalanine wildcard
|
static byte |
G
Glycine byte representation
|
static Wildcard |
G_WILDCARD
Glycine wildcard
|
static byte |
H
Histidine byte representation
|
static Wildcard |
H_WILDCARD
Histidine wildcard
|
static byte |
I
Isoleucine byte representation
|
static Wildcard |
I_WILDCARD
Isoleucine wildcard
|
static byte |
INCOMPLETE_CODON
Incomplete codon byte representation
|
static Wildcard |
INCOMPLETE_CODON_WILDCARD
Incomplete codon wildcard
|
static byte |
J
Leucine or Isoleucine (I or L) byte representation
|
static Wildcard |
J_WILDCARD
Leucine or Isoleucine (I or L) wildcard
|
static byte |
K
Lysine byte representation
|
static Wildcard |
K_WILDCARD
Lysine wildcard
|
static byte |
L
Leucine byte representation
|
static Wildcard |
L_WILDCARD
Leucine wildcard
|
static byte |
M
Methionine byte representation
|
static Wildcard |
M_WILDCARD
Methionine wildcard
|
static byte |
N
Asparagine byte representation
|
static Wildcard |
N_WILDCARD
Asparagine wildcard
|
static byte |
P
Proline byte representation
|
static Wildcard |
P_WILDCARD
Proline wildcard
|
static byte |
Q
Glutamine byte representation
|
static Wildcard |
Q_WILDCARD
Glutamine wildcard
|
static byte |
R
Arginine byte representation
|
static Wildcard |
R_WILDCARD
Arginine wildcard
|
static byte |
S
Serine byte representation
|
static Wildcard |
S_WILDCARD
Serine wildcard
|
static byte |
STOP
Stop codon byte representation
|
static Wildcard |
STOP_WILDCARD
Stop codon wildcard
|
static byte |
T
Threonine byte representation
|
static Wildcard |
T_WILDCARD
Threonine wildcard
|
static byte |
V
Valine byte representation
|
static Wildcard |
V_WILDCARD
Valine wildcard
|
static byte |
W
Tryptophan byte representation
|
static Wildcard |
W_WILDCARD
Tryptophan wildcard
|
static byte |
X
Any amino acid byte representation
|
static Wildcard |
X_WILDCARD
Any amino acid wildcard
|
static byte |
Y
Tyrosine byte representation
|
static Wildcard |
Y_WILDCARD
Tyrosine wildcard
|
static byte |
Z
Glutamine or Glutamic acid (E or Q) byte representation
|
static Wildcard |
Z_WILDCARD
Glutamine or Glutamic acid (E or Q) wildcard
|
| Modifier and Type | Method and Description |
|---|---|
SequenceBuilder<S> |
createBuilder()
Returns a sequence builder for corresponding sequence type.
|
byte |
symbolToCode(char symbol)
Gets the binary code representing given symbol (case insensitive) or -1 if there
is no such symbol in this alphabet
|
basicSize, codeToSymbol, codeToWildcard, equals, getAllWildcards, getAlphabetName, getEmptySequence, getId, getWildcardForAnyLetter, hashCode, isWildcard, maskToWildcard, parse, size, symbolToCodeWithException, symbolToWildcard, toString, writeReplacepublic static final byte STOP
public static final byte A
public static final byte C
public static final byte D
public static final byte E
public static final byte F
public static final byte G
public static final byte H
public static final byte I
public static final byte K
public static final byte L
public static final byte M
public static final byte N
public static final byte P
public static final byte Q
public static final byte R
public static final byte S
public static final byte T
public static final byte V
public static final byte W
public static final byte Y
public static final byte INCOMPLETE_CODON
public static final byte X
public static final byte B
public static final byte J
public static final byte Z
public static final Wildcard STOP_WILDCARD
public static final Wildcard A_WILDCARD
public static final Wildcard C_WILDCARD
public static final Wildcard D_WILDCARD
public static final Wildcard E_WILDCARD
public static final Wildcard F_WILDCARD
public static final Wildcard G_WILDCARD
public static final Wildcard H_WILDCARD
public static final Wildcard I_WILDCARD
public static final Wildcard K_WILDCARD
public static final Wildcard L_WILDCARD
public static final Wildcard M_WILDCARD
public static final Wildcard N_WILDCARD
public static final Wildcard P_WILDCARD
public static final Wildcard Q_WILDCARD
public static final Wildcard R_WILDCARD
public static final Wildcard S_WILDCARD
public static final Wildcard T_WILDCARD
public static final Wildcard V_WILDCARD
public static final Wildcard W_WILDCARD
public static final Wildcard Y_WILDCARD
public static final Wildcard INCOMPLETE_CODON_WILDCARD
public static final Wildcard X_WILDCARD
public static final Wildcard B_WILDCARD
public static final Wildcard J_WILDCARD
public static final Wildcard Z_WILDCARD
public byte symbolToCode(char symbol)
AlphabetsymbolToCode in class Alphabet<AminoAcidSequence>symbol - symbol to convertpublic SequenceBuilder<S> createBuilder()
AlphabetcreateBuilder in class Alphabet<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>Copyright © 2018. All rights reserved.