io.repseq.seqbase

Class LocalFileResolver

java.lang.Object

io.repseq.seqbase.AbstractRAFastaResolver

io.repseq.seqbase.LocalFileResolver

All Implemented Interfaces:

OptionalSequenceResolver, SequenceResolver

public final class LocalFileResolver
extends AbstractRAFastaResolver
implements OptionalSequenceResolver

Constructor Summary

Constructors

Constructor and Description
LocalFileResolver()

Method Summary

Modifier and Type	Method and Description
boolean	canResolve(SequenceAddress address) Returns true if can resolve such address
protected java.nio.file.Path	getFASTAFile(SequenceAddress address) Resolves uri to existing fasta file.
protected com.milaboratory.util.LongProcessReporter	getReporter() Returns instance specific reporter
protected java.lang.String	resolveReaderId(SequenceAddress address) Extracts id to be used as key for reader from original address
protected java.lang.String	resolveRecordId(java.net.URI address) Extracts record name from original address

Methods inherited from class io.repseq.seqbase.AbstractRAFastaResolver

resolve, resolveReader

Methods inherited from class java.lang.Object

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

Methods inherited from interface io.repseq.seqbase.SequenceResolver

resolve

Constructor Detail

LocalFileResolver

public LocalFileResolver()

Method Detail

resolveRecordId

protected java.lang.String resolveRecordId(java.net.URI address)

Description copied from class: AbstractRAFastaResolver

Extracts record name from original address

Specified by:

resolveRecordId in class AbstractRAFastaResolver

Parameters:

address - original address

Returns:

record id

resolveReaderId

protected java.lang.String resolveReaderId(SequenceAddress address)

Description copied from class: AbstractRAFastaResolver

Extracts id to be used as key for reader from original address

Specified by:

resolveReaderId in class AbstractRAFastaResolver

Parameters:

address - original address

Returns:

reader id

getReporter

protected com.milaboratory.util.LongProcessReporter getReporter()

Description copied from class: AbstractRAFastaResolver

Returns instance specific reporter

Specified by:

getReporter in class AbstractRAFastaResolver

Returns:

instance specific reporter

getFASTAFile

protected java.nio.file.Path getFASTAFile(SequenceAddress address)

Description copied from class: AbstractRAFastaResolver

Resolves uri to existing fasta file. E.g. this method performs download.

Specified by:

getFASTAFile in class AbstractRAFastaResolver

Parameters:

address - original uri

Returns:

path to fasta file

canResolve

public boolean canResolve(SequenceAddress address)

Description copied from interface: OptionalSequenceResolver

Returns true if can resolve such address

Specified by:

canResolve in interface OptionalSequenceResolver

Parameters:

address - address

Returns: