com.milaboratory.core.sequence

Class SequencesUtils

java.lang.Object

com.milaboratory.core.sequence.SequencesUtils

public final class SequencesUtils
extends Object

Utility methods for sequences.

Author:

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

Constructor Summary

Constructors

Constructor and Description
SequencesUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static boolean	belongsToAlphabet(Alphabet<?> alphabet, String string) Check if a sequence contains letters only from specified alphabet.
static <S extends Seq<S>> S	concatenate(S... sequences) Returns a concatenation of several sequences.
static NucleotideSequence	convertBit2ArrayToNSequence(Bit2Array bar) Used to read legacy file formats.
static Bit2Array	convertNSequenceToBit2Array(NucleotideSequence seq) Used to write legacy file formats.
static <S extends Sequence<S>> int	mismatchCount(S seq0, int seq0Offset, S seq1, int seq1Offset, int length) Calculates number of mismatches (comparing position by position) between two regions of one or two different sequences.
static Set<Alphabet<?>>	possibleAlphabets(String string) Returns a set of possible alphabets for a given string.
static <S extends Sequence<S>> S	wildcardsToRandomBasic(S sequence, long seed) Converts sequence with wildcards to a sequence without wildcards by converting wildcard letters to uniformly distributed letters from the set of letters allowed by the wildcard.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequencesUtils

public SequencesUtils()

Method Detail

belongsToAlphabet

public static boolean belongsToAlphabet(Alphabet<?> alphabet,
                        String string)

Check if a sequence contains letters only from specified alphabet. So in can be converted to corresponding type of sequence.

Parameters:

alphabet - alphabet

string - string to check

Returns:

true if sequence belongs to alphabet, false if does not

possibleAlphabets

public static Set<Alphabet<?>> possibleAlphabets(String string)

Returns a set of possible alphabets for a given string.

Looks for alphabets registered in Alphabets.

Parameters:

string - target string (sequence)

Returns:

set of possible alphabets for a given string

mismatchCount

public static <S extends Sequence<S>> int mismatchCount(S seq0,
                                        int seq0Offset,
                                        S seq1,
                                        int seq1Offset,
                                        int length)

Calculates number of mismatches (comparing position by position) between two regions of one or two different sequences.

Type Parameters:

S - type of sequence

Parameters:

seq0 - first sequence

seq0Offset - first letter of second region in first sequence

seq1 - second sequence (may be the same as seq0

seq1Offset - first letter of second region in second sequence

length - length of both regions

Returns:

number of mismatches

Throws:

IllegalArgumentException - if one of regions is outside of target sequence

concatenate

public static <S extends Seq<S>> S concatenate(S... sequences)

Returns a concatenation of several sequences.

Type Parameters:

S - type of sequences

Parameters:

sequences - array of sequences

Returns:

concatenation of several sequences

wildcardsToRandomBasic

public static <S extends Sequence<S>> S wildcardsToRandomBasic(S sequence,
                                               long seed)

Converts sequence with wildcards to a sequence without wildcards by converting wildcard letters to uniformly distributed letters from the set of letters allowed by the wildcard. (see Wildcard.getUniformlyDistributedBasicCode(long).

Returns same result for the same combination of sequence and seed.

Type Parameters:

S - type of sequence

Parameters:

sequence - sequence to convert

seed - seed for random generator

Returns:

sequence with wildcards replaced by uniformly distributed random basic letters

convertNSequenceToBit2Array

public static Bit2Array convertNSequenceToBit2Array(NucleotideSequence seq)

Used to write legacy file formats.

Returns:

Bit2Array representation of nucleotide sequence

convertBit2ArrayToNSequence

public static NucleotideSequence convertBit2ArrayToNSequence(Bit2Array bar)

Used to read legacy file formats.

Returns:

NucleotideSequence constructed from Bit2Array