com.milaboratory.core.mutations

Class Mutations<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.mutations.Mutations<S>

All Implemented Interfaces:

Serializable

public final class Mutations<S extends Sequence<S>>
extends Object
implements Serializable

Author:

Dmitry Bolotin, Stanislav Poslavsky

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static Mutations<AminoAcidSequence>	EMPTY_AMINO_ACID_MUTATIONS Identity mutations object for amino acid sequences.
static Mutations<NucleotideSequence>	EMPTY_NUCLEOTIDE_MUTATIONS Identity mutations object for nucleotide sequences.

Constructor Summary

Constructors

Constructor and Description
Mutations(Alphabet<S> alphabet, int... mutations)
Mutations(Alphabet<S> alphabet, IntArrayList mutations)
Mutations(Alphabet<S> alphabet, String encodedMutations)

Method Summary

Methods

Modifier and Type	Method and Description
Mutations<S>	combineWith(Mutations<S> other) Returns combined mutations array (this applied before other).
Mutations<S>	concat(Mutations<S> other) Concatenates this and other
int	convertToSeq1Position(int seq2Position) Converts position from coordinates in seq2 (after mutation) to coordinates in seq1 (before mutation) using this alignment (mutations).
int	convertToSeq2Position(int seq1Position) Converts position from coordinates in seq1 (before mutation) to coordinates in seq2 (after mutation) using this alignment (mutations).
int	countOf(MutationType type)
int	countOfIndels()
static <S extends Sequence<S>> Mutations<S>	decode(String string, Alphabet<S> alphabet)
static Mutations<AminoAcidSequence>	decodeAA(String string)
static Mutations<NucleotideSequence>	decodeNuc(String string)
static <S extends Sequence<S>> Mutations<S>	empty(Alphabet<S> alphabet)
String	encode()
String	encode(String separator)
String	encodeFixed()
boolean	equals(Object o)
Mutations<S>	extractAbsoluteMutationsForRange(int from, int to) Extracts mutations for a range of positions in the original sequence.
Mutations<S>	extractAbsoluteMutationsForRange(Range range) Extracts mutations for a range of positions in the original sequence.
Mutations<S>	extractRelativeMutationsForRange(int from, int to) Extracts mutations for a range of positions in the original sequence and performs shift of corresponding positions (moves them to -from).
Mutations<S>	extractRelativeMutationsForRange(Range range) Extracts mutations for a range of positions in the original sequence and performs shift of corresponding positions (moves them to -range.from).
int	firsMutationPosition()
int	firstMutationWithPosition(int position)
int	firstMutationWithPosition(int fromIndex, int toIndex, int position)
Alphabet<S>	getAlphabet()
byte	getFromAsCodeByIndex(int index)
char	getFromAsSymbolByIndex(int index)
int	getLengthDelta() Returns the difference between the length of initial sequence and length of mutated sequence.
Range	getMutatedRange()
int	getMutation(int index)
int	getPositionByIndex(int index)
Mutations<S>	getRange(int from, int to) Extracts sub mutations by from-to mutation indices.
int[]	getRAWMutations()
int	getRawTypeByIndex(int index)
byte	getToAsCodeByIndex(int index)
char	getToAsSymbolByIndex(int index)
MutationType	getTypeByIndex(int index)
int	hashCode()
Mutations<S>	invert() Inverts mutations, so that they reflect difference from seq2 to seq1.
boolean	isCompatibleWith(S sequence)
boolean	isEmpty()
int	lastMutationPosition()
Mutations<S>	move(int offset) Moves positions of mutations by specified offset
S	mutate(S sequence)
static int	pabs(int position) Converts positions returned by convertToSeq2Position(int) and convertToSeq1Position(int) to a positive number by applying (-1 - x) transformation for negative input values.
Mutations<S>	removeMutationsInRange(int from, int to) Removes mutations for a range of positions in the original sequence and performs shift of corresponding positions of mutations.
Mutations<S>	removeMutationsInRange(Range range) See removeMutationsInRange(int, int).
Mutations<S>	removeMutationsInRanges(Range... ranges) See removeMutationsInRange(int, int).
int	size()
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

EMPTY_NUCLEOTIDE_MUTATIONS

public static final Mutations<NucleotideSequence> EMPTY_NUCLEOTIDE_MUTATIONS

Identity mutations object for nucleotide sequences.

EMPTY_AMINO_ACID_MUTATIONS

public static final Mutations<AminoAcidSequence> EMPTY_AMINO_ACID_MUTATIONS

Identity mutations object for amino acid sequences.

Constructor Detail

Mutations

public Mutations(Alphabet<S> alphabet,
         IntArrayList mutations)

Mutations

public Mutations(Alphabet<S> alphabet,
         String encodedMutations)

Mutations

public Mutations(Alphabet<S> alphabet,
         int... mutations)

Method Detail

size

public int size()

getAlphabet

public Alphabet<S> getAlphabet()

getMutation

public int getMutation(int index)

getRAWMutations

public int[] getRAWMutations()

isEmpty

public boolean isEmpty()

getPositionByIndex

public int getPositionByIndex(int index)

getFromAsCodeByIndex

public byte getFromAsCodeByIndex(int index)

getToAsCodeByIndex

public byte getToAsCodeByIndex(int index)

getFromAsSymbolByIndex

public char getFromAsSymbolByIndex(int index)

getToAsSymbolByIndex

public char getToAsSymbolByIndex(int index)

getRawTypeByIndex

public int getRawTypeByIndex(int index)

getTypeByIndex

public MutationType getTypeByIndex(int index)

isCompatibleWith

public boolean isCompatibleWith(S sequence)

mutate

public S mutate(S sequence)

convertToSeq2Position

public int convertToSeq2Position(int seq1Position)

Converts position from coordinates in seq1 (before mutation) to coordinates in seq2 (after mutation) using this alignment (mutations). If letter in provided position is marked as deleted (deletion) in this mutations, this method will return (- 1 - imagePosition), where imagePosition is a position of letter right after that place where target nucleotide was removed according to this alignment.

Parameters:

seq1Position - position in seq1

Returns:

position in seq2

convertToSeq1Position

public int convertToSeq1Position(int seq2Position)

Converts position from coordinates in seq2 (after mutation) to coordinates in seq1 (before mutation) using this alignment (mutations). If letter in provided position is marked as insertion in this mutations, this method will return (- 1 - imagePosition), where imagePosition is a position of letter right after that place where target nucleotide was added according to this alignment.

Parameters:

seq2Position - position in seq2

Returns:

position in seq1

getLengthDelta

public int getLengthDelta()

Returns the difference between the length of initial sequence and length of mutated sequence. Negative values denotes that mutated sequence is shorter.

Returns:

difference between the length of initial sequence and mutated sequence

concat

public Mutations<S> concat(Mutations<S> other)

Concatenates this and other

combineWith

public Mutations<S> combineWith(Mutations<S> other)

Returns combined mutations array (this applied before other).

Parameters:

other - second mutations object

Returns:

combined mutations

move

public Mutations<S> move(int offset)

Moves positions of mutations by specified offset

Parameters:

offset - offset

Returns:

relocated positions

extractRelativeMutationsForRange

public Mutations<S> extractRelativeMutationsForRange(Range range)

Extracts mutations for a range of positions in the original sequence and performs shift of corresponding positions (moves them to -range.from).

Insertions before range.from excluded. Insertions after (range.to - 1) included.

Important: to extract leftmost insertions (trailing insertions) use range.from = -1.

Parameters:

range - range

Returns:

mutations for a range of positions

extractRelativeMutationsForRange

public Mutations<S> extractRelativeMutationsForRange(int from,
                                            int to)

Extracts mutations for a range of positions in the original sequence and performs shift of corresponding positions (moves them to -from).

Insertions before from excluded. Insertions after (to - 1) included.

Important: to extract leftmost insertions (trailing insertions) use from = -1. E.g. extractRelativeMutationsForRange(mut, -1, seqLength) == mut.

Parameters:

from - left bound of range, inclusive. Use -1 to extract leftmost insertions.

to - right bound of range, exclusive

Returns:

mutations for a range of positions

extractAbsoluteMutationsForRange

public Mutations<S> extractAbsoluteMutationsForRange(Range range)

Extracts mutations for a range of positions in the original sequence.

Insertions before from excluded. Insertions after (to - 1) included.

Important: to extract leftmost insertions (trailing insertions) use range with from = -1.

Parameters:

range - target range in original sequence

Returns:

mutations for a range of positions in original sequence

extractAbsoluteMutationsForRange

public Mutations<S> extractAbsoluteMutationsForRange(int from,
                                            int to)

Extracts mutations for a range of positions in the original sequence.

Insertions before from excluded. Insertions after (to - 1) included.

Important: to extract leftmost insertions (trailing insertions) use from = -1. E.g. extractAbsoluteMutationsForRange(mut, -1, seqLength) == mut.

Parameters:

from - left bound of range, inclusive. Use -1 to extract leftmost insertions.

to - right bound of range, exclusive

Returns:

mutations for a range of positions in original sequence

removeMutationsInRanges

public Mutations<S> removeMutationsInRanges(Range... ranges)

See removeMutationsInRange(int, int).

Ranges must be sorted.

Parameters:

ranges - ranges to remove

removeMutationsInRange

public Mutations<S> removeMutationsInRange(Range range)

See removeMutationsInRange(int, int).

Parameters:

range - range to removes

removeMutationsInRange

public Mutations<S> removeMutationsInRange(int from,
                                  int to)

Removes mutations for a range of positions in the original sequence and performs shift of corresponding positions of mutations.

Insertions before from will be left untouched. Insertions after (to - 1) will be removed.

Important: to remove leftmost insertions (left trailing insertions) use from = -1. E.g. extractRelativeMutationsForRange(mut, -1, seqLength) == mut.

Parameters:

from - left bound of range, inclusive. Use -1 to extract leftmost insertions.

to - right bound of range, exclusive

Returns:

mutations for a range of positions

invert

public Mutations<S> invert()

Inverts mutations, so that they reflect difference from seq2 to seq1.

E.g. for mutations generated with

 NucleotideSequence ref = randomSequence(300);
 int[] mutations = Mutations.generateMutations(ref,
                             MutationModels.getEmpiricalNucleotideMutationModel()
                             .multiply(3.0));
 

and the inverted mutations

 int[] invMutations = ConsensusAligner.invertMutations(mutations);
 

The following two methods are equal

 Mutations.printAlignment(ref, mutations);
 Mutations.printAlignment(Mutations.mutate(ref, mutations), invMutations);
 

Same stands for

 Mutations.getPosition(mutations, posInSeq1)
 

Returns:

mutations that will generate seq1 from seq2

countOfIndels

public int countOfIndels()

countOf

public int countOf(MutationType type)

getRange

public Mutations<S> getRange(int from,
                    int to)

Extracts sub mutations by from-to mutation indices.

Parameters:

from - index in current mutations object pointing to the first mutation to be extracted

to - index in current mutations object pointing to the next after last mutation to be extracted

Returns:

sub mutations

firsMutationPosition

public int firsMutationPosition()

lastMutationPosition

public int lastMutationPosition()

getMutatedRange

public Range getMutatedRange()

toString

public String toString()

Overrides:

toString in class Object

encode

public String encode()

encode

public String encode(String separator)

encodeFixed

public String encodeFixed()

decodeNuc

public static Mutations<NucleotideSequence> decodeNuc(String string)

decodeAA

public static Mutations<AminoAcidSequence> decodeAA(String string)

decode

public static <S extends Sequence<S>> Mutations<S> decode(String string,
                                          Alphabet<S> alphabet)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

pabs

public static int pabs(int position)

Converts positions returned by convertToSeq2Position(int) and convertToSeq1Position(int) to a positive number by applying (-1 - x) transformation for negative input values. So, for non-existing positions (if corresponding letter is absent in the target sequence, like in case of deletion and convertToSeq1Position(int) method) position of the first existing letter in target sequence will be returned.

Parameters:

position - position returned by convertToSeq2Position(int) or convertToSeq1Position(int) methods

Returns:

positive position

firstMutationWithPosition

public int firstMutationWithPosition(int position)

firstMutationWithPosition

public int firstMutationWithPosition(int fromIndex,
                            int toIndex,
                            int position)

empty

public static <S extends Sequence<S>> Mutations<S> empty(Alphabet<S> alphabet)