AbstractFeatureReader (htsjdk 2.14.3 API)

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

Nested Classes
Modifier and Type	Class	Description
`static class`	`AbstractFeatureReader.ComponentMethods`

Field Summary

Fields
Modifier and Type Field Description

static Set<String> BLOCK_COMPRESSED_EXTENSIONS

protected FeatureCodec<T,SOURCE> codec

protected FeatureCodecHeader header

Fields
Modifier and Type	Field	Description
`static Set<String>`	`BLOCK_COMPRESSED_EXTENSIONS`
`protected 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

All Methods Static Methods Instance Methods Concrete Methods
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)`	Whether the name of a file ends in one of the BLOCK_COMPRESSED_EXTENSIONS
`static boolean`	`hasBlockCompressedExtension(String fileName)`	Whether a filename ends in one of the BLOCK_COMPRESSED_EXTENSIONS
`static boolean`	`hasBlockCompressedExtension(URI uri)`	Whether the path of a URI resource ends in one of the BLOCK_COMPRESSED_EXTENSIONS
`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 interface htsjdk.tribble.FeatureReader
close, getSequenceNames, iterator, query, query

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

Field Detail

codec

protected final FeatureCodec<T extends Feature,SOURCE> codec

header
```
protected FeatureCodecHeader header
```

BLOCK_COMPRESSED_EXTENSIONS

public static final Set<String> BLOCK_COMPRESSED_EXTENSIONS

Constructor Detail

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 Detail

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
```
public static boolean hasBlockCompressedExtension(String fileName)
```
Whether a filename ends in one of the BLOCK_COMPRESSED_EXTENSIONS

Parameters:

fileName -

Returns:

hasBlockCompressedExtension
```
public static boolean hasBlockCompressedExtension(File file)
```
Whether the name of a file ends in one of the BLOCK_COMPRESSED_EXTENSIONS

Parameters:

file -

Returns:

hasBlockCompressedExtension
```
public static boolean hasBlockCompressedExtension(URI uri)
```
Whether the path of a URI resource ends in one of the BLOCK_COMPRESSED_EXTENSIONS

Parameters:

uri - a URI representing the resource to check

Returns:

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 interface htsjdk.tribble.FeatureReader

Methods inherited from class java.lang.Object

Field Detail

codec

header

BLOCK_COMPRESSED_EXTENSIONS

Constructor Detail

AbstractFeatureReader

AbstractFeatureReader

Method Detail

getFeatureReader

getFeatureReader

getFeatureReader

getFeatureReader

getFeatureReader

hasIndex

isQueryable

setComponentMethods

hasBlockCompressedExtension

hasBlockCompressedExtension

hasBlockCompressedExtension

getHeader

isTabix