io.repseq.core

Class BaseSequence

java.lang.Object

io.repseq.core.BaseSequence

public class BaseSequence
extends java.lang.Object

DTO for BaseSequence Represents base sequence where V/D/J/C gene is located. Can be anything from a whole chromosome to a small region of some genomic/transcriptomic contig with additional mutations introduced to it (used to represent allelic variants. This object define two optional modification steps for original sequence: (1) cutting of specified regions with subsequent concatenation; (2) application of mutations.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BaseSequence.Deserializer
static class	BaseSequence.Serializer

Constructor Summary

Constructors

Constructor and Description
BaseSequence(java.lang.String origin) Creates non-mutated base sequence from original url.
BaseSequence(java.net.URI origin) Creates non-mutated base sequence from original url.
BaseSequence(java.net.URI origin, com.milaboratory.core.Range[] regions, com.milaboratory.core.mutations.Mutations<com.milaboratory.core.sequence.NucleotideSequence> mutations) Creates BaseSequence object

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
com.milaboratory.core.mutations.Mutations<com.milaboratory.core.sequence.NucleotideSequence>	getMutations()
java.net.URI	getOrigin()
com.milaboratory.core.Range[]	getRegions()
int	hashCode()
boolean	isPureOriginalSequence() Returns true if this object represents original sequence without any modifications
com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence>	resolve(java.nio.file.Path context, SequenceResolver resolver) Returns SequenceProvider to access underlying sequence

Methods inherited from class java.lang.Object

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

Constructor Detail

BaseSequence

public BaseSequence(java.lang.String origin)

Creates non-mutated base sequence from original url. (Pure Original sequence)

Parameters:

origin - url of original sequence

BaseSequence

public BaseSequence(java.net.URI origin)

Creates non-mutated base sequence from original url. (Pure Original sequence)

Parameters:

origin - url of original sequence

BaseSequence

public BaseSequence(java.net.URI origin,
                    com.milaboratory.core.Range[] regions,
                    com.milaboratory.core.mutations.Mutations<com.milaboratory.core.sequence.NucleotideSequence> mutations)

Creates BaseSequence object

Parameters:

origin - original sequence URL

regions - subregions of sequence (mutations applied to this subregions)

mutations - mutations relative to extracted subregions

Method Detail

resolve

public com.milaboratory.core.sequence.provider.SequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> resolve(java.nio.file.Path context,
                                                                                                                           SequenceResolver resolver)

Returns SequenceProvider to access underlying sequence

Parameters:

context - resolution context

resolver - sequence resolver

Returns:

SequenceProvider to access underlying sequence

isPureOriginalSequence

public boolean isPureOriginalSequence()

Returns true if this object represents original sequence without any modifications

Returns:

true if this object represents original sequence without any modifications

getOrigin

public java.net.URI getOrigin()

getRegions

public com.milaboratory.core.Range[] getRegions()

getMutations

public com.milaboratory.core.mutations.Mutations<com.milaboratory.core.sequence.NucleotideSequence> getMutations()

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object