TabixFeatureReader (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.tribble.AbstractFeatureReader<T,SOURCE>
- - htsjdk.tribble.TabixFeatureReader<T,SOURCE>

All Implemented Interfaces:: FeatureReader<T>, Closeable, 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	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)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`close()`	Closes the reader
`List<String>`	`getSequenceNames()`	Provides the list of sequenceNames if known.
`boolean`	`hasIndex()`	Whether the reader has an index or not Default implementation returns false
`CloseableTribbleIterator<T>`	`iterator()`	Provides access to all the features in the reader
`CloseableTribbleIterator<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

Methods inherited from interface htsjdk.tribble.FeatureReader
query

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

- Constructor Detail
  - 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 url
    
    codec -
    
    Throws:
    
    IOException
  - 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 url
    
    indexFile - - path to the index file.
    
    codec -
    
    Throws:
    
    IOException
  - 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 url
    
    indexFile - 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 a Path
    
    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 a Path
    
    Throws:
    
    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:
    
    false
  - 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.
  - 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
  - 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.
  - close
```
public void close()
           throws IOException
```
    Description copied from interface: FeatureReader
    
    Closes the reader
    
    Throws:
    
    IOException

Class TabixFeatureReader<T extends Feature,SOURCE>

Nested Class Summary

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

Field Summary

Fields inherited from class htsjdk.tribble.AbstractFeatureReader

Constructor Summary

Method Summary

Methods inherited from class htsjdk.tribble.AbstractFeatureReader

Methods inherited from interface htsjdk.tribble.FeatureReader

Methods inherited from class java.lang.Object

Constructor Detail

TabixFeatureReader

TabixFeatureReader

TabixFeatureReader

Method Detail

hasIndex

getSequenceNames

query

iterator

close