com.milaboratory.core.sequence

Class AminoAcidAlphabet

java.lang.Object

com.milaboratory.core.sequence.Alphabet<S>

com.milaboratory.core.sequence.AminoAcidAlphabet

All Implemented Interfaces:

Serializable

public final class AminoAcidAlphabet
extends Alphabet<S>

Amino acid alphabet with additional symbols.

"_" represents incomplete codon (residual 1 or 2 nucleotides remaining after translation of all full codons)

Author:

Bolotin Dmitriy (bolotin.dmitriy@gmail.com), Shugay Mikhail (mikhail.shugay@gmail.com)

See Also:

Alphabet, AminoAcidSequence, Sequence, Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.milaboratory.core.sequence.Alphabet

Alphabet.AlphabetSerialization

Field Summary

Fields

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

Method Summary

Methods

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

Methods inherited from class com.milaboratory.core.sequence.Alphabet

basicSize, codeToSymbol, codeToWildcard, equals, getAllWildcards, getAlphabetName, getEmptySequence, getId, getWildcardForAnyLetter, hashCode, isWildcard, maskToWildcard, parse, size, symbolToCodeWithException, symbolToWildcard, toString, writeReplace

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

STOP

public static final byte STOP

Stop codon byte representation

See Also:

Constant Field Values

A

public static final byte A

Alanine byte representation

See Also:

Constant Field Values

C

public static final byte C

Cysteine byte representation

See Also:

Constant Field Values

D

public static final byte D

Aspartic Acid byte representation

See Also:

Constant Field Values

E

public static final byte E

Glutamic Acid representation

See Also:

Constant Field Values

F

public static final byte F

Phenylalanine byte representation

See Also:

Constant Field Values

G

public static final byte G

Glycine byte representation

See Also:

Constant Field Values

H

public static final byte H

Histidine byte representation

See Also:

Constant Field Values

I

public static final byte I

Isoleucine byte representation

See Also:

Constant Field Values

K

public static final byte K

Lysine byte representation

See Also:

Constant Field Values

L

public static final byte L

Leucine byte representation

See Also:

Constant Field Values

M

public static final byte M

Methionine byte representation

See Also:

Constant Field Values

N

public static final byte N

Asparagine byte representation

See Also:

Constant Field Values

P

public static final byte P

Proline byte representation

See Also:

Constant Field Values

Q

public static final byte Q

Glutamine byte representation

See Also:

Constant Field Values

R

public static final byte R

Arginine byte representation

See Also:

Constant Field Values

S

public static final byte S

Serine byte representation

See Also:

Constant Field Values

T

public static final byte T

Threonine byte representation

See Also:

Constant Field Values

V

public static final byte V

Valine byte representation

See Also:

Constant Field Values

W

public static final byte W

Tryptophan byte representation

See Also:

Constant Field Values

Y

public static final byte Y

Tyrosine byte representation

See Also:

Constant Field Values

INCOMPLETE_CODON

public static final byte INCOMPLETE_CODON

Incomplete codon byte representation

See Also:

Constant Field Values

X

public static final byte X

Any amino acid byte representation

See Also:

Constant Field Values

B

public static final byte B

Aspartic acid or Asparagine (N or D) byte representation

See Also:

Constant Field Values

J

public static final byte J

Leucine or Isoleucine (I or L) byte representation

See Also:

Constant Field Values

Z

public static final byte Z

Glutamine or Glutamic acid (E or Q) byte representation

See Also:

Constant Field Values

STOP_WILDCARD

public static final Wildcard STOP_WILDCARD

Stop codon wildcard

A_WILDCARD

public static final Wildcard A_WILDCARD

Alanine wildcard

C_WILDCARD

public static final Wildcard C_WILDCARD

Cysteine wildcard

D_WILDCARD

public static final Wildcard D_WILDCARD

Aspartic Acid wildcard

E_WILDCARD

public static final Wildcard E_WILDCARD

Glutamic Acid wildcard

F_WILDCARD

public static final Wildcard F_WILDCARD

Phenylalanine wildcard

G_WILDCARD

public static final Wildcard G_WILDCARD

Glycine wildcard

H_WILDCARD

public static final Wildcard H_WILDCARD

Histidine wildcard

I_WILDCARD

public static final Wildcard I_WILDCARD

Isoleucine wildcard

K_WILDCARD

public static final Wildcard K_WILDCARD

Lysine wildcard

L_WILDCARD

public static final Wildcard L_WILDCARD

Leucine wildcard

M_WILDCARD

public static final Wildcard M_WILDCARD

Methionine wildcard

N_WILDCARD

public static final Wildcard N_WILDCARD

Asparagine wildcard

P_WILDCARD

public static final Wildcard P_WILDCARD

Proline wildcard

Q_WILDCARD

public static final Wildcard Q_WILDCARD

Glutamine wildcard

R_WILDCARD

public static final Wildcard R_WILDCARD

Arginine wildcard

S_WILDCARD

public static final Wildcard S_WILDCARD

Serine wildcard

T_WILDCARD

public static final Wildcard T_WILDCARD

Threonine wildcard

V_WILDCARD

public static final Wildcard V_WILDCARD

Valine wildcard

W_WILDCARD

public static final Wildcard W_WILDCARD

Tryptophan wildcard

Y_WILDCARD

public static final Wildcard Y_WILDCARD

Tyrosine wildcard

INCOMPLETE_CODON_WILDCARD

public static final Wildcard INCOMPLETE_CODON_WILDCARD

Incomplete codon wildcard

X_WILDCARD

public static final Wildcard X_WILDCARD

Any amino acid wildcard

B_WILDCARD

public static final Wildcard B_WILDCARD

Aspartic acid or Asparagine (N or D) wildcard

J_WILDCARD

public static final Wildcard J_WILDCARD

Leucine or Isoleucine (I or L) wildcard

Z_WILDCARD

public static final Wildcard Z_WILDCARD

Glutamine or Glutamic acid (E or Q) wildcard

Method Detail

symbolToCode

public byte symbolToCode(char symbol)

Description copied from class: Alphabet

Gets the binary code representing given symbol (case insensitive) or -1 if there is no such symbol in this alphabet

Overrides:

symbolToCode in class Alphabet<AminoAcidSequence>

Parameters:

symbol - symbol to convert

Returns:

binary code of the symbol (case insensitive) or -1 if there is no such symbol in the alphabet

createBuilder

public SequenceBuilder<S> createBuilder()

Description copied from class: Alphabet

Returns a sequence builder for corresponding sequence type.

Specified by:

createBuilder in class Alphabet<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

Returns:

sequence builder for corresponding sequence type