htsjdk.tribble

Class AbstractFeatureReader<T extends Feature,SOURCE>

java.lang.Object

htsjdk.tribble.AbstractFeatureReader<T,SOURCE>

All Implemented Interfaces:

FeatureReader<T>, java.io.Closeable, java.lang.AutoCloseable

Direct Known Subclasses:

TabixFeatureReader, TribbleIndexedFeatureReader

public abstract class AbstractFeatureReader<T extends Feature,SOURCE>
extends java.lang.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 and Description
static class	AbstractFeatureReader.ComponentMethods

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.Set<java.lang.String>	BLOCK_COMPRESSED_EXTENSIONS
protected FeatureCodec<T,SOURCE>	codec
protected FeatureCodecHeader	header

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractFeatureReader(java.lang.String path, FeatureCodec<T,SOURCE> codec)

Method Summary

Modifier and Type	Method and Description
static <FEATURE extends Feature,SOURCE> AbstractFeatureReader<FEATURE,SOURCE>	getFeatureReader(java.lang.String featureFile, FeatureCodec<FEATURE,SOURCE> codec) Calls getFeatureReader(String, FeatureCodec, boolean) with requireIndex = true
static <FEATURE extends Feature,SOURCE> AbstractFeatureReader<FEATURE,SOURCE>	getFeatureReader(java.lang.String featureResource, FeatureCodec<FEATURE,SOURCE> codec, boolean requireIndex) getFeatureReader(String, String, FeatureCodec, boolean) with null for indexResource
static <FEATURE extends Feature,SOURCE> AbstractFeatureReader<FEATURE,SOURCE>	getFeatureReader(java.lang.String featureResource, FeatureCodec<FEATURE,SOURCE> codec, Index index) Return a reader with a supplied index.
static <FEATURE extends Feature,SOURCE> AbstractFeatureReader<FEATURE,SOURCE>	getFeatureReader(java.lang.String featureResource, java.lang.String indexResource, FeatureCodec<FEATURE,SOURCE> codec, boolean requireIndex)
java.lang.Object	getHeader() get the header
static boolean	hasBlockCompressedExtension(java.io.File file) Whether the name of a file ends in one of the BLOCK_COMPRESSED_EXTENSIONS
static boolean	hasBlockCompressedExtension(java.lang.String fileName) Whether a filename ends in one of the BLOCK_COMPRESSED_EXTENSIONS
boolean	hasIndex() Whether the reader has an index or not Default implementation returns false
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

Field Detail

codec

protected final FeatureCodec<T extends Feature,SOURCE> codec

header

protected FeatureCodecHeader header

BLOCK_COMPRESSED_EXTENSIONS

public static final java.util.Set<java.lang.String> BLOCK_COMPRESSED_EXTENSIONS

Constructor Detail

AbstractFeatureReader

protected AbstractFeatureReader(java.lang.String path,
                                FeatureCodec<T,SOURCE> codec)

Method Detail

getFeatureReader

public static <FEATURE extends Feature,SOURCE> AbstractFeatureReader<FEATURE,SOURCE> getFeatureReader(java.lang.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(java.lang.String featureResource,
                                                                                                      FeatureCodec<FEATURE,SOURCE> codec,
                                                                                                      boolean requireIndex)
                                                                                               throws TribbleException

getFeatureReader(String, String, FeatureCodec, boolean) with null for indexResource

Throws:

TribbleException

getFeatureReader

public static <FEATURE extends Feature,SOURCE> AbstractFeatureReader<FEATURE,SOURCE> getFeatureReader(java.lang.String featureResource,
                                                                                                      java.lang.String indexResource,
                                                                                                      FeatureCodec<FEATURE,SOURCE> codec,
                                                                                                      boolean requireIndex)
                                                                                               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 -

requireIndex - whether an index is required for this file

Returns:

Throws:

TribbleException

getFeatureReader

public static <FEATURE extends Feature,SOURCE> AbstractFeatureReader<FEATURE,SOURCE> getFeatureReader(java.lang.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:

setComponentMethods

public static void setComponentMethods(AbstractFeatureReader.ComponentMethods methods)

hasBlockCompressedExtension

public static boolean hasBlockCompressedExtension(java.lang.String fileName)

Whether a filename ends in one of the BLOCK_COMPRESSED_EXTENSIONS

Parameters:

fileName -

Returns:

hasBlockCompressedExtension

public static boolean hasBlockCompressedExtension(java.io.File file)

Whether the name of a file ends in one of the BLOCK_COMPRESSED_EXTENSIONS

Parameters:

file -

Returns:

getHeader

public java.lang.Object getHeader()

get the header

Specified by:

getHeader in interface FeatureReader<T extends Feature>

Returns:

the header object we've read-in