htsjdk.tribble

Class TabixFeatureReader<T extends Feature,SOURCE>

java.lang.Object

htsjdk.tribble.AbstractFeatureReader<T,SOURCE>

htsjdk.tribble.TabixFeatureReader<T,SOURCE>

All Implemented Interfaces:

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

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

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
TabixFeatureReader(java.lang.String featureFile, AsciiFeatureCodec codec)
TabixFeatureReader(java.lang.String featureFile, java.lang.String indexFile, AsciiFeatureCodec codec)

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
java.util.List<java.lang.String>	getSequenceNames()
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 iterator over all features overlapping the given interval

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

TabixFeatureReader

public TabixFeatureReader(java.lang.String featureFile,
                  AsciiFeatureCodec codec)
                   throws java.io.IOException

Parameters:

featureFile - - path to a feature file. Can be a local file, http url, or ftp url

codec -

Throws:

java.io.IOException

TabixFeatureReader

public TabixFeatureReader(java.lang.String featureFile,
                  java.lang.String indexFile,
                  AsciiFeatureCodec codec)
                   throws java.io.IOException

Parameters:

featureFile - - path to a feature file. Can be a local file, http url, or ftp url

indexFile - - path to the index file.

codec -

Throws:

java.io.IOException

Method Detail

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:

getSequenceNames

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

query

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

Return iterator over all features overlapping the given interval

Parameters:

chr -

start -

end -

Returns:

Throws:

java.io.IOException

iterator

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

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Throws:

java.io.IOException