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

All Implemented Interfaces:

FeatureReader<T>, Closeable, 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	Description
`TribbleIndexedFeatureReader(String featurePath, FeatureCodec<T,SOURCE> codec, boolean requireIndex)`
`TribbleIndexedFeatureReader(String featurePath, FeatureCodec<T,SOURCE> codec, boolean requireIndex, Function<SeekableByteChannel,SeekableByteChannel> wrapper, Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)`
`TribbleIndexedFeatureReader(String featureFile, FeatureCodec<T,SOURCE> codec, Index index)`
`TribbleIndexedFeatureReader(String featureFile, String indexFile, FeatureCodec<T,SOURCE> codec, boolean requireIndex)`
`TribbleIndexedFeatureReader(String featureFile, String indexFile, FeatureCodec<T,SOURCE> codec, boolean requireIndex, 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()`	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
`boolean`	`isQueryable()`
`CloseableTribbleIterator<T>`	`iterator()`	Provides access to all the features in the reader
`CloseableTribbleIterator<T>`	`query(String chr, int start, int end)`	Return an iterator to iterate over features overlapping the specified interval

Methods inherited from class htsjdk.tribble.AbstractFeatureReader
getFeatureReader, getFeatureReader, getFeatureReader, getFeatureReader, getFeatureReader, getHeader, hasBlockCompressedExtension, hasBlockCompressedExtension, hasBlockCompressedExtension, isTabix, setComponentMethods

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
query

- Constructor Detail
  - TribbleIndexedFeatureReader
```
public TribbleIndexedFeatureReader(String featurePath,
                                   FeatureCodec<T,SOURCE> codec,
                                   boolean requireIndex)
                            throws 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:
    
    IOException
  - TribbleIndexedFeatureReader
```
public TribbleIndexedFeatureReader(String featurePath,
                                   FeatureCodec<T,SOURCE> codec,
                                   boolean requireIndex,
                                   Function<SeekableByteChannel,SeekableByteChannel> wrapper,
                                   Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)
                            throws IOException
```
    Throws:
    
    IOException
  - TribbleIndexedFeatureReader
```
public TribbleIndexedFeatureReader(String featureFile,
                                   String indexFile,
                                   FeatureCodec<T,SOURCE> codec,
                                   boolean requireIndex)
                            throws 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:
    
    IOException
  - TribbleIndexedFeatureReader
```
public TribbleIndexedFeatureReader(String featureFile,
                                   String indexFile,
                                   FeatureCodec<T,SOURCE> codec,
                                   boolean requireIndex,
                                   Function<SeekableByteChannel,SeekableByteChannel> wrapper,
                                   Function<SeekableByteChannel,SeekableByteChannel> indexWrapper)
                            throws IOException
```
    Parameters:
    
    featureFile - - path to the feature file, can be a local file path, http url, or ftp url, or any other uri supported by a Path plugin
    
    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:
    
    IOException
  - TribbleIndexedFeatureReader
```
public TribbleIndexedFeatureReader(String featureFile,
                                   FeatureCodec<T,SOURCE> codec,
                                   Index index)
                            throws 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:
    
    IOException
- Method Detail
  - close
```
public void close()
           throws IOException
```
    Description copied from interface: FeatureReader
    
    Closes the reader
    
    Throws:
    
    IOException
  - getSequenceNames
```
public List<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:
    
    false
  - isQueryable
```
public boolean isQueryable()
```
    Specified by:
    
    isQueryable in interface FeatureReader<T extends Feature>
    
    Overrides:
    
    isQueryable in class AbstractFeatureReader<T extends Feature,SOURCE>
    
    Returns:
    
    true if the reader has an index, which means that it can be queried.
  - query
```
public CloseableTribbleIterator<T> query(String chr,
                                         int start,
                                         int end)
                                  throws 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:
    
    IOException
  - iterator
```
public CloseableTribbleIterator<T> iterator()
                                     throws IOException
```
    Description copied from interface: FeatureReader
    
    Provides access to all the features in the reader
    
    Returns:
    
    Return an iterator to iterate over the entire file
    
    Throws:
    
    IOException

Class TribbleIndexedFeatureReader<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 class java.lang.Object

Methods inherited from interface htsjdk.tribble.FeatureReader

Constructor Detail

TribbleIndexedFeatureReader

TribbleIndexedFeatureReader

TribbleIndexedFeatureReader

TribbleIndexedFeatureReader

TribbleIndexedFeatureReader

Method Detail

close

getSequenceNames

hasIndex

isQueryable

query

iterator

Class TribbleIndexedFeatureReader<T extends Feature,SOURCE>