AutoCloseable
, Closeable
FastaSequenceFile
, IndexedFastaSequenceFile
, SRAIndexedSequenceFile
public interface ReferenceSequenceFile extends Closeable
Modifier and Type | Method | Description |
---|---|---|
void |
close() |
|
ReferenceSequence |
getSequence(String contig) |
Retrieves the complete sequence described by this contig.
|
SAMSequenceDictionary |
getSequenceDictionary() |
Must return a sequence dictionary with at least the following fields completed
for each sequence: name, length.
|
ReferenceSequence |
getSubsequenceAt(String contig,
long start,
long stop) |
Gets the subsequence of the contig in the range [start,stop]
|
boolean |
isIndexed() |
|
ReferenceSequence |
nextSequence() |
Retrieves the next whole sequences from the file.
|
void |
reset() |
Resets the ReferenceSequenceFile so that the next call to nextSequence() will return
the first sequence in the file.
|
String |
toString() |
SAMSequenceDictionary getSequenceDictionary()
ReferenceSequence nextSequence()
void reset()
boolean isIndexed()
ReferenceSequence getSequence(String contig)
contig
- contig whose data should be returned.UnsupportedOperationException
- if !sIndexed.ReferenceSequence getSubsequenceAt(String contig, long start, long stop)
contig
- Contig whose subsequence to retrieve.start
- inclusive, 1-based start of region.stop
- inclusive, 1-based stop of region.UnsupportedOperationException
- if !sIndexed.String toString()
void close() throws IOException
close
in interface AutoCloseable
close
in interface Closeable
IOException