Package htsjdk.tribble

Class AbstractFeatureReader<T extends Feature,SOURCE>

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