com.milaboratory.core.sequence

Class NucleotideAlphabet

java.lang.Object

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

com.milaboratory.core.sequence.NucleotideAlphabet

All Implemented Interfaces:

Serializable

public final class NucleotideAlphabet
extends Alphabet<S>

An alphabet for nucleotide sequences. This alphabet defines the following mapping:

0 - 'A', 1 - 'G', 2 - 'C', 3 - 'T'

This class also defines wildcards as specified by IUPAC: 'R' for 'A' or 'G', 'Y' for 'C' or 'T' etc.

Author:

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

See Also:

Alphabet, NucleotideSequence, 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 Adenine byte representation
static Wildcard	A_WILDCARD Adenine byte representation
static byte	B not A (B comes after A)
static Wildcard	B_WILDCARD not A (B comes after A)
static byte	C Cytosine byte representation
static Wildcard	C_WILDCARD Cytosine byte representation
static byte	D not C (D comes after C)
static Wildcard	D_WILDCARD not C (D comes after C)
static byte	G Guanine byte representation
static Wildcard	G_WILDCARD Guanine byte representation
static byte	H not G (H comes after G)
static Wildcard	H_WILDCARD not G (H comes after G)
static byte	K Keto
static Wildcard	K_WILDCARD Keto
static byte	M aMino
static Wildcard	M_WILDCARD aMino
static byte	N any Nucleotide
static Wildcard	N_WILDCARD any Nucleotide
static byte	R puRine
static Wildcard	R_WILDCARD puRine
static byte	S Strong
static Wildcard	S_WILDCARD Strong
static byte	T Thymine byte representation
static Wildcard	T_WILDCARD Thymine byte representation
static byte	V not T (V comes after T and U)
static Wildcard	V_WILDCARD not T (V comes after T and U)
static byte	W Weak
static Wildcard	W_WILDCARD Weak
static byte	Y pYrimidine
static Wildcard	Y_WILDCARD pYrimidine

Method Summary

Methods

Modifier and Type	Method and Description
static byte	byteSymbolToCode(byte symbol)
static byte	complementCode(byte code) Returns a complementary nucleotide code.
static byte	complementCode(Wildcard wildcard) Returns a complementary nucleotide code.
static Wildcard	complementWildcard(byte code) Returns a complementary wildcard object
static Wildcard	complementWildcard(Wildcard wildcard) Returns a complementary wildcard object
SequenceBuilder<S>	createBuilder() Returns a sequence builder for corresponding sequence type.
static byte	symbolByteFromCode(byte code) Returns UTF-8 character corresponding to specified byte-code.

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

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

Methods inherited from class java.lang.Object

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

Field Detail

A

public static final byte A

Adenine byte representation

See Also:

Constant Field Values

G

public static final byte G

Guanine byte representation

See Also:

Constant Field Values

C

public static final byte C

Cytosine byte representation

See Also:

Constant Field Values

T

public static final byte T

Thymine byte representation

See Also:

Constant Field Values

N

public static final byte N

any Nucleotide

See Also:

Constant Field Values

R

public static final byte R

puRine

See Also:

Constant Field Values

Y

public static final byte Y

pYrimidine

See Also:

Constant Field Values

S

public static final byte S

Strong

See Also:

Constant Field Values

W

public static final byte W

Weak

See Also:

Constant Field Values

K

public static final byte K

Keto

See Also:

Constant Field Values

M

public static final byte M

aMino

See Also:

Constant Field Values

B

public static final byte B

not A (B comes after A)

See Also:

Constant Field Values

D

public static final byte D

not C (D comes after C)

See Also:

Constant Field Values

H

public static final byte H

not G (H comes after G)

See Also:

Constant Field Values

V

public static final byte V

not T (V comes after T and U)

See Also:

Constant Field Values

A_WILDCARD

public static final Wildcard A_WILDCARD

Adenine byte representation

G_WILDCARD

public static final Wildcard G_WILDCARD

Guanine byte representation

C_WILDCARD

public static final Wildcard C_WILDCARD

Cytosine byte representation

T_WILDCARD

public static final Wildcard T_WILDCARD

Thymine byte representation

N_WILDCARD

public static final Wildcard N_WILDCARD

any Nucleotide

R_WILDCARD

public static final Wildcard R_WILDCARD

puRine

Y_WILDCARD

public static final Wildcard Y_WILDCARD

pYrimidine

S_WILDCARD

public static final Wildcard S_WILDCARD

Strong

W_WILDCARD

public static final Wildcard W_WILDCARD

Weak

K_WILDCARD

public static final Wildcard K_WILDCARD

Keto

M_WILDCARD

public static final Wildcard M_WILDCARD

aMino

B_WILDCARD

public static final Wildcard B_WILDCARD

not A (B comes after A)

D_WILDCARD

public static final Wildcard D_WILDCARD

not C (D comes after C)

H_WILDCARD

public static final Wildcard H_WILDCARD

not G (H comes after G)

V_WILDCARD

public static final Wildcard V_WILDCARD

not T (V comes after T and U)

Method Detail

complementCode

public static byte complementCode(byte code)

Returns a complementary nucleotide code.

Parameters:

code - byte code of nucleotide

Returns:

complementary nucleotide code

complementCode

public static byte complementCode(Wildcard wildcard)

Returns a complementary nucleotide code.

Parameters:

wildcard - wildcard to convert to complementary code

Returns:

complementary nucleotide code

complementWildcard

public static Wildcard complementWildcard(byte code)

Returns a complementary wildcard object

Parameters:

code - byte code of nucleotide

Returns:

complementary wildcard object

complementWildcard

public static Wildcard complementWildcard(Wildcard wildcard)

Returns a complementary wildcard object

Parameters:

wildcard - wildcard to convert to complementary

Returns:

complementary wildcard object

symbolByteFromCode

public static byte symbolByteFromCode(byte code)

Returns UTF-8 character corresponding to specified byte-code.

Parameters:

code - byte-code of nucleotide

Returns:

UTF-8 character corresponding to specified byte-code

byteSymbolToCode

public static byte byteSymbolToCode(byte symbol)

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