htsjdk.beta.codecs.hapref.fasta

Class FASTADecoderV1_0

java.lang.Object

htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0

All Implemented Interfaces:

HaploidReferenceDecoder, HtsDecoder<SAMSequenceDictionary,ReferenceSequence>, HtsQuery<ReferenceSequence>, java.io.Closeable, java.lang.AutoCloseable, java.lang.Iterable<ReferenceSequence>

public class FASTADecoderV1_0
extends java.lang.Object
implements HaploidReferenceDecoder

The v1.0 FASTA decoder.

Field Summary

Fields

Modifier and Type	Field and Description
protected Bundle	inputBundle

Constructor Summary

Constructors

Constructor and Description
FASTADecoderV1_0(Bundle inputBundle)

Method Summary

Modifier and Type	Method and Description
void	close() Close any resources associated with this decoder.
java.lang.String	getDisplayName() Get a user-friendly display name for this decoder.
java.lang.String	getFileFormat() Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (see BundleResourceType and BundleResource.getFileFormat()).
SAMSequenceDictionary	getHeader() Get the file header for this decoder.
ReferenceSequenceFile	getReferenceSequenceFile()
HtsVersion	getVersion() Get the version of the file format supported by this decoder.
boolean	hasIndex() Return true if the underlying resource has an index.
boolean	isQueryable() Gte true if the underlying resource is queryable.
CloseableIterator<ReferenceSequence>	iterator() Get an iterator of all records in the underlying resource.

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery

query, query, query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping, queryStart

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

inputBundle

protected Bundle inputBundle

Constructor Detail

FASTADecoderV1_0

public FASTADecoderV1_0(Bundle inputBundle)

Method Detail

getDisplayName

public java.lang.String getDisplayName()

Description copied from interface: HtsDecoder

Get a user-friendly display name for this decoder.

Specified by:

getDisplayName in interface HtsDecoder<SAMSequenceDictionary,ReferenceSequence>

Returns:

a user-friendly display name for this decoder for use in error and warning messages

getFileFormat

public final java.lang.String getFileFormat()

Description copied from interface: HtsDecoder

Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (see BundleResourceType and BundleResource.getFileFormat()).

Specified by:

getFileFormat in interface HtsDecoder<SAMSequenceDictionary,ReferenceSequence>

Returns:

the name of the underlying file format handled by this decoder

getHeader

public SAMSequenceDictionary getHeader()

Description copied from interface: HtsDecoder

Get the file header for this decoder.

Specified by:

getHeader in interface HtsDecoder<SAMSequenceDictionary,ReferenceSequence>

Returns:

the file header for this decoder, of type H

getVersion

public HtsVersion getVersion()

Description copied from interface: HtsDecoder

Get the version of the file format supported by this decoder.

Specified by:

getVersion in interface HtsDecoder<SAMSequenceDictionary,ReferenceSequence>

iterator

public CloseableIterator<ReferenceSequence> iterator()

Description copied from interface: HtsQuery

Get an iterator of all records in the underlying resource.

Specified by:

iterator in interface HtsQuery<ReferenceSequence>

Specified by:

iterator in interface java.lang.Iterable<ReferenceSequence>

Returns:

an iterator of all records in the underlying resource

isQueryable

public boolean isQueryable()

Description copied from interface: HtsQuery

Gte true if the underlying resource is queryable.

Specified by:

isQueryable in interface HtsQuery<ReferenceSequence>

Returns:

true if the underlying resource is queryable. this may be true even if the underlying resource returns false for HtsQuery.hasIndex()

hasIndex

public boolean hasIndex()

Description copied from interface: HtsQuery

Return true if the underlying resource has an index.

Specified by:

hasIndex in interface HtsQuery<ReferenceSequence>

Returns:

true if the underlying resource has an index

getReferenceSequenceFile

@InternalAPI
public ReferenceSequenceFile getReferenceSequenceFile()

close

public void close()

Description copied from interface: HtsDecoder

Close any resources associated with this decoder.

Specified by:

close in interface HtsDecoder<SAMSequenceDictionary,ReferenceSequence>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable