java.lang.Object

htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0

All Implemented Interfaces:: HaploidReferenceDecoder, HtsDecoder<SAMSequenceDictionary,ReferenceSequence>, HtsQuery<ReferenceSequence>, Closeable, AutoCloseable, Iterable<ReferenceSequence>

public class FASTADecoderV1_0 extends Object implements HaploidReferenceDecoder

The v1.0 FASTA decoder.

Field Summary

Fields

Modifier and Type

Field

Description

protected Bundle

inputBundle
Constructor Summary

Constructors

Constructor

Description

FASTADecoderV1_0(Bundle inputBundle)
Method Summary

Modifier and Type

Method

Description

void

close()

Close any resources associated with this decoder.

String

getDisplayName()

Get a user-friendly display name for this decoder.

final 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 Details
- inputBundle
  
  protected Bundle inputBundle
Constructor Details
- FASTADecoderV1_0
  
  public FASTADecoderV1_0(Bundle inputBundle)
Method Details
- getDisplayName
  
  public 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 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 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 AutoCloseable
  
  Specified by:
  
  close in interface Closeable
  
  Specified by:
  
  close in interface HtsDecoder<SAMSequenceDictionary,ReferenceSequence>

Class FASTADecoderV1_0

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

Field Details

inputBundle

Constructor Details

FASTADecoderV1_0

Method Details

getDisplayName

getFileFormat

getHeader

getVersion

iterator

isQueryable

hasIndex

getReferenceSequenceFile

close