java.lang.Object

htsjdk.tribble.AbstractFeatureReader<T,SOURCE>

All Implemented Interfaces:: FeatureReader<T>, Closeable, AutoCloseable

Direct Known Subclasses:: TabixFeatureReader, TribbleIndexedFeatureReader

public abstract class AbstractFeatureReader<T extends Feature,SOURCE> extends Object implements FeatureReader<T>

jrobinso

the feature reader class, which uses indices and codecs to read in Tribble file formats.

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

static class

AbstractFeatureReader.ComponentMethods
Field Summary

Fields

Modifier and Type

Field

Description

static final Set<String>

BLOCK_COMPRESSED_EXTENSIONS

Deprecated.
since June 2019 use FileExtensions.BLOCK_COMPRESSED instead.

protected final FeatureCodec<T,SOURCE>

codec

protected FeatureCodecHeader

header
Constructor Summary

Constructors

Modifier

Constructor

Description

protected

AbstractFeatureReader(String path, FeatureCodec<T,SOURCE> codec)

protected

AbstractFeatureReader(String path, FeatureCodec<T,SOURCE> codec, Function<SeekableByteChannel,SeekableByteChannel> wrapper, Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)
Method Summary

Modifier and Type

Method

Description

static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE,SOURCE>

getFeatureReader(String featureFile, FeatureCodec<FEATURE,SOURCE> codec)

Calls getFeatureReader(String, FeatureCodec, boolean) with requireIndex = true

static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE,SOURCE>

getFeatureReader(String featureResource, FeatureCodec<FEATURE,SOURCE> codec, boolean requireIndex)

getFeatureReader(String, String, FeatureCodec, boolean, Function, Function) with null for indexResource, wrapper, and indexWrapper

static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE,SOURCE>

getFeatureReader(String featureResource, FeatureCodec<FEATURE,SOURCE> codec, Index index)

Return a reader with a supplied index.

static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE,SOURCE>

getFeatureReader(String featureResource, String indexResource, FeatureCodec<FEATURE,SOURCE> codec, boolean requireIndex)

getFeatureReader(String, String, FeatureCodec, boolean, Function, Function) with null for wrapper, and indexWrapper

static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE,SOURCE>

getFeatureReader(String featureResource, String indexResource, FeatureCodec<FEATURE,SOURCE> codec, boolean requireIndex, Function<SeekableByteChannel,SeekableByteChannel> wrapper, Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)

Object

getHeader()

get the header

static boolean

hasBlockCompressedExtension(File file)

Deprecated.
use IOUtil.hasBlockCompressedExtension(File).

static boolean

hasBlockCompressedExtension(String fileName)

Deprecated.
use IOUtil.hasBlockCompressedExtension(String).

static boolean

hasBlockCompressedExtension(URI uri)

Deprecated.
use IOUtil.hasBlockCompressedExtension(URI).

boolean

hasIndex()

Whether the reader has an index or not Default implementation returns false

boolean

isQueryable()

static boolean

isTabix(String resourcePath, String indexPath)

static void

setComponentMethods(AbstractFeatureReader.ComponentMethods methods)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.tribble.FeatureReader
close, getSequenceNames, iterator, query, query

Field Details
- codec
  
  protected final FeatureCodec<T extends Feature,SOURCE> codec
- header
  
  protected FeatureCodecHeader header
- BLOCK_COMPRESSED_EXTENSIONS
  
  @Deprecated public static final Set<String> BLOCK_COMPRESSED_EXTENSIONS
  
  Deprecated.
  since June 2019 use FileExtensions.BLOCK_COMPRESSED instead.
Constructor Details
- AbstractFeatureReader
  
  protected AbstractFeatureReader(String path, FeatureCodec<T,SOURCE> codec)
- AbstractFeatureReader
  
  protected AbstractFeatureReader(String path, FeatureCodec<T,SOURCE> codec, Function<SeekableByteChannel,SeekableByteChannel> wrapper, Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)
Method Details
- getFeatureReader
  
  public static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE,SOURCE> getFeatureReader(String featureFile, FeatureCodec<FEATURE,SOURCE> codec) throws TribbleException
  
  Calls getFeatureReader(String, FeatureCodec, boolean) with requireIndex = true
  
  Throws:
  
  TribbleException
- getFeatureReader
  
  public static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE,SOURCE> getFeatureReader(String featureResource, FeatureCodec<FEATURE,SOURCE> codec, boolean requireIndex) throws TribbleException
  
  getFeatureReader(String, String, FeatureCodec, boolean, Function, Function) with null for indexResource, wrapper, and indexWrapper
  
  Throws:
  
  TribbleException
- getFeatureReader
  
  public static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE,SOURCE> getFeatureReader(String featureResource, String indexResource, FeatureCodec<FEATURE,SOURCE> codec, boolean requireIndex) throws TribbleException
  
  getFeatureReader(String, String, FeatureCodec, boolean, Function, Function) with null for wrapper, and indexWrapper
  
  Throws:
  
  TribbleException
- getFeatureReader
  
  public static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE,SOURCE> getFeatureReader(String featureResource, String indexResource, FeatureCodec<FEATURE,SOURCE> codec, boolean requireIndex, Function<SeekableByteChannel,SeekableByteChannel> wrapper, Function<SeekableByteChannel,SeekableByteChannel> indexWrapper) throws TribbleException
  
  Parameters:
  
  featureResource - the feature file to create from
  
  indexResource - the index for the feature file. If null, will auto-generate (if necessary)
  
  codec - the codec to use to decode the individual features
  
  requireIndex - whether an index is required for this file
  
  wrapper - a wrapper to apply to the byte stream from the featureResource allowing injecting features like caching and prefetching of the stream, may be null, will only be applied if featureResource is a uri representing a Path
  
  indexWrapper - a wrapper to apply to the byte stream from the indexResource, may be null, will only be applied if indexResource is a uri representing a Path
  
  Throws:
  
  TribbleException
- getFeatureReader
  
  public static <FEATURE extends Feature, SOURCE> AbstractFeatureReader<FEATURE,SOURCE> getFeatureReader(String featureResource, FeatureCodec<FEATURE,SOURCE> codec, Index index) throws TribbleException
  
  Return a reader with a supplied index.
  
  Parameters:
  
  featureResource - the path to the source file containing the features
  
  codec - used to decode the features
  
  index - index of featureResource
  
  Returns:
  
  a reader for this data
  
  Throws:
  
  TribbleException
- hasIndex
  
  public boolean hasIndex()
  
  Whether the reader has an index or not Default implementation returns false
  
  Returns:
  
  false
- isQueryable
  
  public boolean isQueryable()
  
  Specified by:
  
  isQueryable in interface FeatureReader<T extends Feature>
  
  Returns:
  
  true if the reader has an index, which means that it can be queried.
- setComponentMethods
  
  public static void setComponentMethods(AbstractFeatureReader.ComponentMethods methods)
- hasBlockCompressedExtension
  
  @Deprecated public static boolean hasBlockCompressedExtension(String fileName)
  
  Deprecated.
  use IOUtil.hasBlockCompressedExtension(String).
- hasBlockCompressedExtension
  
  @Deprecated public static boolean hasBlockCompressedExtension(File file)
  
  Deprecated.
  use IOUtil.hasBlockCompressedExtension(File).
- hasBlockCompressedExtension
  
  @Deprecated public static boolean hasBlockCompressedExtension(URI uri)
  
  Deprecated.
  use IOUtil.hasBlockCompressedExtension(URI).
- getHeader
  
  public Object getHeader()
  
  get the header
  
  Specified by:
  
  getHeader in interface FeatureReader<T extends Feature>
  
  Returns:
  
  the header object we've read-in
- isTabix
  
  public static boolean isTabix(String resourcePath, String indexPath) throws IOException
  
  Throws:
  
  IOException

Class AbstractFeatureReader<T extends Feature,SOURCE>

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.tribble.FeatureReader

Field Details

codec

header

BLOCK_COMPRESSED_EXTENSIONS

Constructor Details

AbstractFeatureReader

AbstractFeatureReader

Method Details

getFeatureReader

getFeatureReader

getFeatureReader

getFeatureReader

getFeatureReader

hasIndex

isQueryable

setComponentMethods

hasBlockCompressedExtension

hasBlockCompressedExtension

hasBlockCompressedExtension

getHeader

isTabix