Package htsjdk.tribble
Interface FeatureReader<T extends Feature>
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- Type Parameters:
T
- a feature type
- All Superinterfaces:
AutoCloseable
,Closeable
- All Known Implementing Classes:
AbstractFeatureReader
,TabixFeatureReader
,TribbleIndexedFeatureReader
public interface FeatureReader<T extends Feature> extends Closeable
the basic interface that feature sources need to match
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Method Summary
All Methods Instance Methods Abstract Methods Default Methods Modifier and Type Method Description void
close()
Closes the readerObject
getHeader()
Provide access to the header of the readerList<String>
getSequenceNames()
Provides the list of sequenceNames if known.default boolean
isQueryable()
CloseableTribbleIterator<T>
iterator()
Provides access to all the features in the readerdefault CloseableTribbleIterator<T>
query(Locatable locus)
Query the reader for a particular interval corresponding to a contig and a 1-based closedCloseableTribbleIterator<T>
query(String chr, int start, int end)
Query the reader for a particular interval corresponding to a contig and a 1-based closed
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Method Detail
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query
CloseableTribbleIterator<T> query(String chr, int start, int end) throws IOException
Query the reader for a particular interval corresponding to a contig and a 1-based closed- Parameters:
chr
- the contig to be queriedstart
- the start of the interval (1-based) to be queriedend
- the last base in the interval to be queried- Returns:
- an iterator containing the features that at in the interval.
- Throws:
IOException
- If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.
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query
default CloseableTribbleIterator<T> query(Locatable locus) throws IOException
Query the reader for a particular interval corresponding to a contig and a 1-based closed- Parameters:
locus
- The locus to be queried- Returns:
- an iterator containing the features that at in the interval.
- Throws:
IOException
- If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.
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iterator
CloseableTribbleIterator<T> iterator() throws IOException
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
void close() throws IOException
Closes the reader- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Throws:
IOException
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getSequenceNames
List<String> getSequenceNames()
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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getHeader
Object getHeader()
Provide access to the header of the reader- Returns:
- the header of the reader. May be null.
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isQueryable
default boolean isQueryable()
- Returns:
- true if the reader has an index, which means that it can be queried.
Must be implemented to return true if the implementation supports
query(Locatable)
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