Package htsjdk.tribble
Class TabixFeatureReader<T extends Feature,SOURCE>
- java.lang.Object
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- htsjdk.tribble.AbstractFeatureReader<T,SOURCE>
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- htsjdk.tribble.TabixFeatureReader<T,SOURCE>
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- All Implemented Interfaces:
FeatureReader<T>
,Closeable
,AutoCloseable
public class TabixFeatureReader<T extends Feature,SOURCE> extends AbstractFeatureReader<T,SOURCE>
- Since:
- 2/11/12
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Nested Class Summary
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Nested classes/interfaces inherited from class htsjdk.tribble.AbstractFeatureReader
AbstractFeatureReader.ComponentMethods
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Field Summary
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Fields inherited from class htsjdk.tribble.AbstractFeatureReader
BLOCK_COMPRESSED_EXTENSIONS, codec, header
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Constructor Summary
Constructors Constructor Description TabixFeatureReader(String featureFile, AsciiFeatureCodec codec)
TabixFeatureReader(String featureFile, String indexFile, AsciiFeatureCodec codec)
TabixFeatureReader(String featureFile, String indexFile, AsciiFeatureCodec codec, Function<SeekableByteChannel,SeekableByteChannel> wrapper, Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
Closes the readerList<String>
getSequenceNames()
Provides the list of sequenceNames if known.boolean
hasIndex()
Whether the reader has an index or not Default implementation returns falseCloseableTribbleIterator<T>
iterator()
Provides access to all the features in the readerCloseableTribbleIterator<T>
query(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, getFeatureReader, getHeader, hasBlockCompressedExtension, hasBlockCompressedExtension, hasBlockCompressedExtension, isQueryable, isTabix, setComponentMethods
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface htsjdk.tribble.FeatureReader
query
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Constructor Detail
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TabixFeatureReader
public TabixFeatureReader(String featureFile, AsciiFeatureCodec codec) throws IOException
- Parameters:
featureFile
- - path to a feature file. Can be a local file, http url, or ftp urlcodec
-- Throws:
IOException
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TabixFeatureReader
public TabixFeatureReader(String featureFile, String indexFile, AsciiFeatureCodec codec) throws IOException
- Parameters:
featureFile
- - path to a feature file. Can be a local file, http url, or ftp urlindexFile
- - path to the index file.codec
-- Throws:
IOException
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TabixFeatureReader
public TabixFeatureReader(String featureFile, String indexFile, AsciiFeatureCodec codec, Function<SeekableByteChannel,SeekableByteChannel> wrapper, Function<SeekableByteChannel,SeekableByteChannel> indexWrapper) throws IOException
- Parameters:
featureFile
- path to a feature file. Can be a local file, http url, or ftp urlindexFile
- path to the index 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 featureFile is a uri representing aPath
indexWrapper
- a wrapper to apply to the byte stream from the indexResource, may be null, will only be applied if indexFile is a uri representing aPath
- Throws:
IOException
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Method Detail
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hasIndex
public boolean hasIndex()
Description copied from class:AbstractFeatureReader
Whether the reader has an index or not Default implementation returns false- Overrides:
hasIndex
in classAbstractFeatureReader<T extends Feature,SOURCE>
- Returns:
- false
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getSequenceNames
public List<String> getSequenceNames()
Description copied from interface:FeatureReader
Provides the list of sequenceNames if known. Otherwise will return an empty list.- Returns:
- the list of sequenceNames if known. Otherwise will return an empty list.
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query
public CloseableTribbleIterator<T> query(String chr, int start, int end) throws IOException
Return iterator over all features overlapping the given interval- Parameters:
chr
-start
-end
-- Returns:
- Throws:
IOException
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iterator
public CloseableTribbleIterator<T> iterator() throws IOException
Description copied from interface:FeatureReader
Provides access to all the features in the reader- Returns:
- an iterator to all the features in the reader
- Throws:
IOException
- If there's a problem reading.
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close
public void close() throws IOException
Description copied from interface:FeatureReader
Closes the reader- Throws:
IOException
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