htsjdk.tribble

Class TribbleIndexedFeatureReader<T extends Feature,SOURCE>

java.lang.Object

htsjdk.tribble.AbstractFeatureReader<T,SOURCE>

htsjdk.tribble.TribbleIndexedFeatureReader<T,SOURCE>

All Implemented Interfaces:

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

public class TribbleIndexedFeatureReader<T extends Feature,SOURCE>
extends AbstractFeatureReader<T,SOURCE>

A reader for text feature files (i.e. not tabix files). This includes tribble-indexed and non-indexed files. If index both iterate() and query() methods are supported.

Note: Non-indexed files can be gzipped, but not bgzipped.

Since:

2/11/12

Nested Class Summary

Nested classes/interfaces inherited from class htsjdk.tribble.AbstractFeatureReader

AbstractFeatureReader.ComponentMethods

Field Summary

Fields inherited from class htsjdk.tribble.AbstractFeatureReader

BLOCK_COMPRESSED_EXTENSIONS, codec, header

Constructor Summary

Constructors

Constructor and Description
TribbleIndexedFeatureReader(java.lang.String featurePath, FeatureCodec<T,SOURCE> codec, boolean requireIndex)
TribbleIndexedFeatureReader(java.lang.String featureFile, FeatureCodec<T,SOURCE> codec, Index index)
TribbleIndexedFeatureReader(java.lang.String featureFile, java.lang.String indexFile, FeatureCodec<T,SOURCE> codec, boolean requireIndex)

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
java.util.List<java.lang.String>	getSequenceNames() Return the sequence (chromosome/contig) names in this file, if known.
boolean	hasIndex() Whether the reader has an index or not Default implementation returns false
CloseableTribbleIterator<T>	iterator()
CloseableTribbleIterator<T>	query(java.lang.String chr, int start, int end) Return an iterator to iterate over features overlapping the specified interval Note that TribbleIndexedFeatureReader only supports issuing and manipulating a single query for each reader.

Methods inherited from class htsjdk.tribble.AbstractFeatureReader

getFeatureReader, getFeatureReader, getFeatureReader, getFeatureReader, getHeader, hasBlockCompressedExtension, hasBlockCompressedExtension, setComponentMethods

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TribbleIndexedFeatureReader

public TribbleIndexedFeatureReader(java.lang.String featurePath,
                           FeatureCodec<T,SOURCE> codec,
                           boolean requireIndex)
                            throws java.io.IOException

Parameters:

featurePath - - path to the feature file, can be a local file path, http url, or ftp url

codec - - codec to decode the features

requireIndex - - true if the reader will be queries for specific ranges. An index (idx) file must exist

Throws:

java.io.IOException

TribbleIndexedFeatureReader

public TribbleIndexedFeatureReader(java.lang.String featureFile,
                           java.lang.String indexFile,
                           FeatureCodec<T,SOURCE> codec,
                           boolean requireIndex)
                            throws java.io.IOException

Parameters:

featureFile - - path to the feature file, can be a local file path, http url, or ftp url

indexFile - - path to the index file

codec - - codec to decode the features

requireIndex - - true if the reader will be queries for specific ranges. An index (idx) file must exist

Throws:

java.io.IOException

TribbleIndexedFeatureReader

public TribbleIndexedFeatureReader(java.lang.String featureFile,
                           FeatureCodec<T,SOURCE> codec,
                           Index index)
                            throws java.io.IOException

Parameters:

featureFile - - path to the feature file, can be a local file path, http url, or ftp url

codec - - codec to decode the features

index - - a tribble Index object

Throws:

java.io.IOException

Method Detail

close

public void close()
           throws java.io.IOException

Throws:

java.io.IOException

getSequenceNames

public java.util.List<java.lang.String> getSequenceNames()

Return the sequence (chromosome/contig) names in this file, if known.

Returns:

list of strings of the contig names

hasIndex

public boolean hasIndex()

Description copied from class: AbstractFeatureReader

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

Overrides:

hasIndex in class AbstractFeatureReader<T extends Feature,SOURCE>

Returns:

query

public CloseableTribbleIterator<T> query(java.lang.String chr,
                                int start,
                                int end)
                                                  throws java.io.IOException

Return an iterator to iterate over features overlapping the specified interval

Note that TribbleIndexedFeatureReader only supports issuing and manipulating a single query for each reader. That is, the behavior of the following code is undefined:

reader = new TribbleIndexedFeatureReader() Iterator it1 = reader.query("x", 10, 20) Iterator it2 = reader.query("x", 1000, 1010)

As a consequence of this, the TribbleIndexedFeatureReader are also not thread-safe.

Parameters:

chr - contig

start - start position

end - end position

Returns:

an iterator of records in this interval

Throws:

java.io.IOException

iterator

public CloseableTribbleIterator<T> iterator()
                                                     throws java.io.IOException

Returns:

Return an iterator to iterate over the entire file

Throws:

java.io.IOException