io.repseq.seqbase

Class AbstractRAFastaResolver

java.lang.Object

io.repseq.seqbase.AbstractRAFastaResolver

All Implemented Interfaces:

SequenceResolver

Direct Known Subclasses:

HTTPFastaSequenceResolver, LocalFileResolver

public abstract class AbstractRAFastaResolver
extends java.lang.Object
implements SequenceResolver

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractRAFastaResolver(boolean deleteOnError)

Method Summary

Modifier and Type	Method and Description
protected abstract java.nio.file.Path	getFASTAFile(SequenceAddress uri) Resolves uri to existing fasta file.
protected abstract com.milaboratory.util.LongProcessReporter	getReporter() Returns instance specific reporter
com.milaboratory.core.sequence.provider.CachedSequenceProvider<com.milaboratory.core.sequence.NucleotideSequence>	resolve(SequenceAddress address) Resolves address and returns corresponding
com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader<com.milaboratory.core.sequence.NucleotideSequence>	resolveReader(SequenceAddress address)
protected abstract java.lang.String	resolveReaderId(SequenceAddress address) Extracts id to be used as key for reader from original address
protected abstract java.lang.String	resolveRecordId(java.net.URI address) Extracts record name from original address

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractRAFastaResolver

protected AbstractRAFastaResolver(boolean deleteOnError)

Method Detail

resolveRecordId

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

Extracts record name from original address

Parameters:

address - original address

Returns:

record id

resolveReaderId

protected abstract java.lang.String resolveReaderId(SequenceAddress address)

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

Parameters:

address - original address

Returns:

reader id

getReporter

protected abstract com.milaboratory.util.LongProcessReporter getReporter()

Returns instance specific reporter

Returns:

instance specific reporter

getFASTAFile

protected abstract java.nio.file.Path getFASTAFile(SequenceAddress uri)

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

Parameters:

uri - original uri

Returns:

path to fasta file

resolveReader

public com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader<com.milaboratory.core.sequence.NucleotideSequence> resolveReader(SequenceAddress address)

resolve

public com.milaboratory.core.sequence.provider.CachedSequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> resolve(SequenceAddress address)

Description copied from interface: SequenceResolver

Resolves address and returns corresponding

Specified by:

resolve in interface SequenceResolver

Parameters:

address - address

Returns:

record