public class SRAIndexedSequenceFile extends java.lang.Object implements ReferenceSequenceFile
| Modifier and Type | Field and Description |
|---|---|
protected SAMSequenceDictionary |
sequenceDictionary |
| Constructor and Description |
|---|
SRAIndexedSequenceFile(SRAAccession acc) |
| 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() |
protected SAMSequenceDictionary |
loadSequenceDictionary() |
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.
|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waittoStringprotected SAMSequenceDictionary sequenceDictionary
public SRAIndexedSequenceFile(SRAAccession acc)
acc - accessionpublic SAMSequenceDictionary getSequenceDictionary()
ReferenceSequenceFilegetSequenceDictionary in interface ReferenceSequenceFilepublic ReferenceSequence nextSequence()
ReferenceSequenceFilenextSequence in interface ReferenceSequenceFilepublic void reset()
ReferenceSequenceFilereset in interface ReferenceSequenceFilepublic boolean isIndexed()
isIndexed in interface ReferenceSequenceFilepublic ReferenceSequence getSequence(java.lang.String contig)
ReferenceSequenceFilegetSequence in interface ReferenceSequenceFilecontig - contig whose data should be returned.public ReferenceSequence getSubsequenceAt(java.lang.String contig, long start, long stop)
ReferenceSequenceFilegetSubsequenceAt in interface ReferenceSequenceFilecontig - Contig whose subsequence to retrieve.start - inclusive, 1-based start of region.stop - inclusive, 1-based stop of region.public void close()
throws java.io.IOException
close in interface ReferenceSequenceFileclose in interface java.io.Closeableclose in interface java.lang.AutoCloseablejava.io.IOExceptionprotected SAMSequenceDictionary loadSequenceDictionary() throws ngs.ErrorMsg
ngs.ErrorMsg