com.milaboratory.core.sequence

Class AminoAcidSequence

java.lang.Object

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

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

com.milaboratory.core.sequence.AminoAcidSequence

All Implemented Interfaces:

HasSequence<AminoAcidSequence>, Seq<AminoAcidSequence>, Serializable, Comparable<AminoAcidSequence>

public final class AminoAcidSequence
extends Sequence<S>

Representation of amino acid sequences. Methods for translating nucleotide to amino acid and vice versa are placed in GeneticCode

Author:

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

See Also:

Sequence, AminoAcidAlphabet, GeneticCode, Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AminoAcidSequence.AminoAcidSequencePosition This class represents mapping of nucleotide sequence position onto translated amino acid sequence.

Field Summary

Fields

Modifier and Type	Field and Description
static AminoAcidAlphabet	ALPHABET Amino acid alphabet
protected byte[]	data
static AminoAcidSequence	EMPTY Empty sequence

Constructor Summary

Constructors

Constructor and Description
AminoAcidSequence(byte[] data) Creates sequence with specified data.
AminoAcidSequence(String sequence) Creates amino acid sequence from its string representation (case insensitive).

Method Summary

Methods

Modifier and Type	Method and Description
byte[]	asArray() Returns an array of bytes that encodes this sequence.
byte	codeAt(int position) Returns letter code at specified position.
boolean	containStops() Returns whether this sequence contains stop codons
static int	convertAAPositionToNt(int aaPosition, int ntSequenceLength, TranslationParameters translationParameters)
static int	convertAAPositionToNtFromCenter(int aaPosition, int ntSequenceLength)
static int	convertAAPositionToNtFromLeft(int aaPosition, int ntSequenceLength)
static int	convertAAPositionToNtFromRight(int aaPosition, int ntSequenceLength)
static AminoAcidSequence.AminoAcidSequencePosition	convertNtPositionToAA(int ntPosition, int ntSequenceLength, TranslationParameters translationParameters)
static AminoAcidSequence.AminoAcidSequencePosition	convertNtPositionToAAFromCenter(int ntPosition, int ntSequenceLength) Converts position from nucleotide to amino acid sequence if it was translated using translateFromCenter(NucleotideSequence).
static AminoAcidSequence.AminoAcidSequencePosition	convertNtPositionToAAFromLeft(int ntPosition, int ntSequenceLength) Converts position from nucleotide to amino acid sequence if it was translated using translateFromLeft(NucleotideSequence).
static AminoAcidSequence.AminoAcidSequencePosition	convertNtPositionToAAFromRight(int ntPosition, int ntSequenceLength) Converts position from nucleotide to amino acid sequence if it was translated using translateFromRight(NucleotideSequence).
protected static byte[]	dataFromChars(Alphabet alphabet, char[] chars)
boolean	equals(Object o)
AminoAcidAlphabet	getAlphabet() Returns the alphabet corresponding to this type of sequence.
static byte	getAminoAcid(NucleotideSequence nSequence, int tripletStart) Returns amino acid encoded by triplet starting from specified position (in terms of standard genetic code)
S	getRange(int from, int to) Returns a subsequence of this starting at from (inclusive) and ending at to (exclusive).
static int	getTriplet(NucleotideSequence nSequence, int tripletStart) Extracts int representation of triplet starting from specified position (see implementation for details).
int	hashCode()
int	numberOfStops() Returns the number of stop codons that contained in this sequence
int	size() Returns size of this sequence
static AminoAcidSequence	translate(NucleotideSequence sequence) Translates sequence having length divisible by 3, starting from first nucleotide.
static AminoAcidSequence	translate(NucleotideSequence sequence, int frame) Translate sequence in one of frames (-1, -2, -3 frames are not implemented, use NucleotideSequence.getReverseComplement()) discarding all incomplete codons on both boundaries.
static AminoAcidSequence	translate(NucleotideSequence ns, TranslationParameters translationParameters) Use one of specialized method instead: translateFromLeft(NucleotideSequence) translateFromRight(NucleotideSequence) translateFromCenter(NucleotideSequence)
static AminoAcidSequence	translateFromCenter(NucleotideSequence ns) Translates sequence from both sides, so the first nucleotide of the first triplet matches first nucleotide of the sequence, and last (3rd) nucleotide of last triplet matches last nucleotide of the sequence.
static AminoAcidSequence	translateFromLeft(NucleotideSequence ns) Translates sequence from the left side, so the first nucleotide of the first triplet matches first nucleotide of the sequence.
static AminoAcidSequence	translateFromRight(NucleotideSequence ns) Translates sequence from the right side, so the last (3rd) nucleotide of last triplet matches last nucleotide of the sequence.

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

compareTo, containWildcards, getBuilder, getSequence, indexOf, symbolAt, toMotif, toString

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

concatenate, getRange

Methods inherited from class java.lang.Object

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

Field Detail

EMPTY

public static final AminoAcidSequence EMPTY

Empty sequence

ALPHABET

public static final AminoAcidAlphabet ALPHABET

Amino acid alphabet

data

protected final byte[] data

Constructor Detail

AminoAcidSequence

public AminoAcidSequence(byte[] data)

Creates sequence with specified data.

Parameters:

data - byte array of amino acid codes from alphabet

AminoAcidSequence

public AminoAcidSequence(String sequence)

Creates amino acid sequence from its string representation (case insensitive).

Parameters:

sequence - string representation of amino acid sequence (case insensitive)

Throws:

IllegalArgumentException - if sequence contains unknown amino acid symbol

Method Detail

getAlphabet

public AminoAcidAlphabet getAlphabet()

Description copied from class: Sequence

Returns the alphabet corresponding to this type of sequence.

Returns:

alphabet corresponding to this type of sequence

containStops

public boolean containStops()

Returns whether this sequence contains stop codons

Returns:

whether this sequence contains stop codons

numberOfStops

public int numberOfStops()

Returns the number of stop codons that contained in this sequence

Returns:

number of stop codons that contained in this sequence

getTriplet

public static int getTriplet(NucleotideSequence nSequence,
             int tripletStart)

Extracts int representation of triplet starting from specified position (see implementation for details).

Parameters:

nSequence - nucleotide sequence

tripletStart - position of first nucleotide of triplet

Returns:

int representation of triplet

getAminoAcid

public static byte getAminoAcid(NucleotideSequence nSequence,
                int tripletStart)

Returns amino acid encoded by triplet starting from specified position (in terms of standard genetic code)

Parameters:

nSequence - nucleotide sequence

tripletStart - position of first nucleotide of triplet

Returns:

byte-code of encoded amino acid

translate

public static AminoAcidSequence translate(NucleotideSequence sequence,
                          int frame)

Translate sequence in one of frames (-1, -2, -3 frames are not implemented, use NucleotideSequence.getReverseComplement()) discarding all incomplete codons on both boundaries.

Parameters:

sequence - nucleotide sequence to translate

frame - frame (1, 2 or 3)

Returns:

translated amino acid sequence

translate

public static AminoAcidSequence translate(NucleotideSequence sequence)

Translates sequence having length divisible by 3, starting from first nucleotide.

Parameters:

sequence - nucleotide sequence

Returns:

translated amino acid sequence

convertAAPositionToNt

public static int convertAAPositionToNt(int aaPosition,
                        int ntSequenceLength,
                        TranslationParameters translationParameters)

convertAAPositionToNtFromCenter

public static int convertAAPositionToNtFromCenter(int aaPosition,
                                  int ntSequenceLength)

convertAAPositionToNtFromLeft

public static int convertAAPositionToNtFromLeft(int aaPosition,
                                int ntSequenceLength)

convertAAPositionToNtFromRight

public static int convertAAPositionToNtFromRight(int aaPosition,
                                 int ntSequenceLength)

convertNtPositionToAA

public static AminoAcidSequence.AminoAcidSequencePosition convertNtPositionToAA(int ntPosition,
                                                                int ntSequenceLength,
                                                                TranslationParameters translationParameters)

convertNtPositionToAAFromRight

public static AminoAcidSequence.AminoAcidSequencePosition convertNtPositionToAAFromRight(int ntPosition,
                                                                         int ntSequenceLength)

Converts position from nucleotide to amino acid sequence if it was translated using translateFromRight(NucleotideSequence).

Parameters:

ntPosition - position in nucleotide sequence

ntSequenceLength - length of nucleotide sequence

Returns:

position in amino acid sequence

convertNtPositionToAAFromLeft

public static AminoAcidSequence.AminoAcidSequencePosition convertNtPositionToAAFromLeft(int ntPosition,
                                                                        int ntSequenceLength)

Converts position from nucleotide to amino acid sequence if it was translated using translateFromLeft(NucleotideSequence).

Parameters:

ntPosition - position in nucleotide sequence

ntSequenceLength - length of nucleotide sequence

Returns:

position in amino acid sequence

convertNtPositionToAAFromCenter

public static AminoAcidSequence.AminoAcidSequencePosition convertNtPositionToAAFromCenter(int ntPosition,
                                                                          int ntSequenceLength)

Converts position from nucleotide to amino acid sequence if it was translated using translateFromCenter(NucleotideSequence).

Parameters:

ntPosition - position in nucleotide sequence

ntSequenceLength - length of nucleotide sequence

Returns:

position in amino acid sequence

translate

public static AminoAcidSequence translate(NucleotideSequence ns,
                          TranslationParameters translationParameters)

Use one of specialized method instead:

• translateFromLeft(NucleotideSequence)
• translateFromRight(NucleotideSequence)
• translateFromCenter(NucleotideSequence)

translateFromRight

public static AminoAcidSequence translateFromRight(NucleotideSequence ns)

Translates sequence from the right side, so the last (3rd) nucleotide of last triplet matches last nucleotide of the sequence. Incomplete codon added at the first position of resulting amino acid sequence if initial nucleotide sequence length is not divisible by 3.

 Example for sequence: ATGTCACA

  AT GTC ACA
  _   V   T
 

Parameters:

ns - nucleotide sequence to translate

Returns:

result of translation (see description)

translateFromLeft

public static AminoAcidSequence translateFromLeft(NucleotideSequence ns)

Translates sequence from the left side, so the first nucleotide of the first triplet matches first nucleotide of the sequence. Incomplete codon added at the last position of resulting amino acid sequence if initial nucleotide sequence length is not divisible by 3.

 Example for sequence: ATTAGACA

  ATT AGA CA
   I   R   _
 

Parameters:

ns - nucleotide sequence to translate

Returns:

result of translation (see description)

translateFromCenter

public static AminoAcidSequence translateFromCenter(NucleotideSequence ns)

Translates sequence from both sides, so the first nucleotide of the first triplet matches first nucleotide of the sequence, and last (3rd) nucleotide of last triplet matches last nucleotide of the sequence. Incomplete codon added in the middle of resulting amino acid sequence if initial nucleotide sequence length is not divisible by 3. This method is useful for CDR3 translation? as it preserves original aa sequences of germline V/J genes in case of out-of-frame assemblies.

 Example for sequence: ATTAGACA

  ATT AG  ACA
   I   _   T
 

Parameters:

ns - nucleotide sequence to translate

Returns:

result of translation (see description)

codeAt

public byte codeAt(int position)

Description copied from class: Sequence

Returns letter code at specified position.

Specified by:

codeAt in class Sequence<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

Parameters:

position - position in sequence

Returns:

element at specified position

size

public int size()

Description copied from interface: Seq

Returns size of this sequence

Specified by:

size in interface Seq<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

Returns:

size of this sequence

asArray

public byte[] asArray()

Description copied from class: Sequence

Returns an array of bytes that encodes this sequence.

Overrides:

asArray in class Sequence<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

Returns:

array of bytes that encodes this sequence

getRange

public S getRange(int from,
         int to)

Description copied from interface: Seq

Returns a subsequence of this starting at from (inclusive) and ending at to (exclusive).

Specified by:

getRange in interface Seq<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

Parameters:

from - starting point of subsequence (inclusive)

to - ending point of subsequence (exclusive)

Returns:

subsequence of this starting at from (inclusive) and ending at to (exclusive)

equals

public final boolean equals(Object o)

Overrides:

equals in class Sequence<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

hashCode

public final int hashCode()

Overrides:

hashCode in class Sequence<S extends com.milaboratory.core.sequence.AbstractArraySequence<S>>

dataFromChars

protected static byte[] dataFromChars(Alphabet alphabet,
                   char[] chars)