com.milaboratory.core.sequence

Interface Seq<S extends Seq<S>>

Type Parameters:

S - type of seq (type of extending class)

All Known Subinterfaces:

NSeq<S>

All Known Implementing Classes:

AbstractSeq, AminoAcidSequence, NSequenceWithQuality, NucleotideSequence, Sequence, SequenceQuality

public interface Seq<S extends Seq<S>>

Common interface for all objects representing sequence-like objects like (parent of all subtypes of Sequence; SequenceQuality; SequenceWithQuality)

Method Summary

Methods

Modifier and Type	Method and Description
S	concatenate(S other) Returns a concatenation of this and other sequence (so this will be followed by other in the result).
SeqBuilder<S>	getBuilder() Returns a builder for corresponding seq type.
S	getRange(int from, int to) Returns a subsequence of this starting at from (inclusive) and ending at to (exclusive).
S	getRange(Range range) Returns a subsequence of this bounded by specified range.
int	size() Returns size of this sequence

Method Detail

getRange

S getRange(Range range)

Returns a subsequence of this bounded by specified range.

Parameters:

range - a range that defines starting (inclusive) and ending (exclusive) points of subsequence

Returns:

subsequence of this bounded by specified range.

Throws:

IndexOutOfBoundsException - if from orj to is out of this sequence range

getRange

S getRange(int from,
         int to)

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

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)

Throws:

IndexOutOfBoundsException - if from or to is out of this sequence range

IllegalArgumentException - if from >= to

size

int size()

Returns size of this sequence

Returns:

size of this sequence

getBuilder

SeqBuilder<S> getBuilder()

Returns a builder for corresponding seq type.

Returns:

builder for corresponding seq type

concatenate

S concatenate(S other)

Returns a concatenation of this and other sequence (so this will be followed by other in the result).

Parameters:

other - other sequence

Returns:

concatenation of this and other sequences