public interface ReferenceSequenceFile
extends java.io.Closeable
Modifier and Type | Method and Description |
---|---|
void |
close() |
ReferenceSequence |
getSequence(java.lang.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(java.lang.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.
|
java.lang.String |
toString() |
SAMSequenceDictionary getSequenceDictionary()
ReferenceSequence nextSequence()
void reset()
boolean isIndexed()
ReferenceSequence getSequence(java.lang.String contig)
contig
- contig whose data should be returned.java.lang.UnsupportedOperationException
- if !sIndexed.ReferenceSequence getSubsequenceAt(java.lang.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.java.lang.UnsupportedOperationException
- if !sIndexed.java.lang.String toString()
toString
in class java.lang.Object
void close() throws java.io.IOException
close
in interface java.lang.AutoCloseable
close
in interface java.io.Closeable
java.io.IOException