T
- a feature typeAutoCloseable
, Closeable
AbstractFeatureReader
, TabixFeatureReader
, TribbleIndexedFeatureReader
public interface FeatureReader<T extends Feature> extends Closeable
Modifier and Type | Method | Description |
---|---|---|
void |
close() |
Closes the reader
|
Object |
getHeader() |
Provide access to the header of the reader
|
List<String> |
getSequenceNames() |
Provides the list of sequenceNames if known.
|
default boolean |
isQueryable() |
|
CloseableTribbleIterator<T> |
iterator() |
Provides access to all the features in the reader
|
default CloseableTribbleIterator<T> |
query(Locatable locus) |
Query the reader for a particular interval corresponding to a contig and a 1-based closed
|
CloseableTribbleIterator<T> |
query(String chr,
int start,
int end) |
Query the reader for a particular interval corresponding to a contig and a 1-based closed
|
CloseableTribbleIterator<T> query(String chr, int start, int end) throws IOException
chr
- the contig to be queriedstart
- the start of the interval (1-based) to be queriedend
- the last base in the interval to be queriedIOException
- If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.default CloseableTribbleIterator<T> query(Locatable locus) throws IOException
locus
- The locus to be queriedIOException
- If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.CloseableTribbleIterator<T> iterator() throws IOException
IOException
- If there's a problem reading.void close() throws IOException
close
in interface AutoCloseable
close
in interface Closeable
IOException
List<String> getSequenceNames()
Object getHeader()
default boolean isQueryable()
query(Locatable)