io.repseq.seqbase

Class HTTPFastaSequenceResolver

java.lang.Object

io.repseq.seqbase.AbstractRAFastaResolver

io.repseq.seqbase.HTTPFastaSequenceResolver

All Implemented Interfaces:

OptionalSequenceResolver, SequenceResolver

Direct Known Subclasses:

HTTPSequenceResolvers.NucCoreResolver, HTTPSequenceResolvers.RAWHTTPResolver

public abstract class HTTPFastaSequenceResolver
extends AbstractRAFastaResolver
implements OptionalSequenceResolver

Field Summary

Fields

Modifier and Type	Field and Description
static int	CHUNK_SIZE

Constructor Summary

Constructors

Constructor and Description
HTTPFastaSequenceResolver(HTTPResolversContext context)

Method Summary

Modifier and Type	Method and Description
protected void	ensureCacheDirExist()
java.nio.file.Path	getCacheDir()
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	resolveCacheFileName(java.net.URI address) Resolves HTTP address to file name
protected abstract java.net.URI	resolveHTTPAddress(java.net.URI address) Resolves address to http/https link
protected java.lang.String	resolveReaderId(SequenceAddress address) Extracts id to be used as key for reader from original address

Methods inherited from class io.repseq.seqbase.AbstractRAFastaResolver

resolve, resolveReader, resolveRecordId

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.OptionalSequenceResolver

canResolve

Methods inherited from interface io.repseq.seqbase.SequenceResolver

resolve

Field Detail

CHUNK_SIZE

public static final int CHUNK_SIZE

See Also:

Constant Field Values

Constructor Detail

HTTPFastaSequenceResolver

public HTTPFastaSequenceResolver(HTTPResolversContext context)

Method Detail

getCacheDir

public java.nio.file.Path getCacheDir()

ensureCacheDirExist

protected void ensureCacheDirExist()

resolveHTTPAddress

protected abstract java.net.URI resolveHTTPAddress(java.net.URI address)

Resolves address to http/https link

Parameters:

address - original address

Returns:

http/https link

resolveCacheFileName

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

Resolves HTTP address to file name

Parameters:

address - initialAddress

Returns:

file name

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

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

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