htsjdk.samtools.sra

Class SRAIndexedSequenceFile

java.lang.Object

htsjdk.samtools.sra.SRAIndexedSequenceFile

All Implemented Interfaces:

ReferenceSequenceFile, java.io.Closeable, java.lang.AutoCloseable

public class SRAIndexedSequenceFile
extends java.lang.Object
implements ReferenceSequenceFile

Allows reading Reference data from SRA

Field Summary

Fields

Modifier and Type	Field and Description
protected SAMSequenceDictionary	sequenceDictionary

Constructor Summary

Constructors

Constructor and Description
SRAIndexedSequenceFile(SRAAccession acc)

Method Summary

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.reference.ReferenceSequenceFile

toString

Field Detail

sequenceDictionary

protected SAMSequenceDictionary sequenceDictionary

Constructor Detail

SRAIndexedSequenceFile

public SRAIndexedSequenceFile(SRAAccession acc)

Parameters:

acc - accession

Method Detail

getSequenceDictionary

public SAMSequenceDictionary getSequenceDictionary()

Description copied from interface: ReferenceSequenceFile

Must return a sequence dictionary with at least the following fields completed for each sequence: name, length.

Specified by:

getSequenceDictionary in interface ReferenceSequenceFile

Returns:

a list of sequence records representing the sequences in this reference file

nextSequence

public ReferenceSequence nextSequence()

Description copied from interface: ReferenceSequenceFile

Retrieves the next whole sequences from the file.

Specified by:

nextSequence in interface ReferenceSequenceFile

Returns:

a ReferenceSequence or null if at the end of the file

reset

public void reset()

Description copied from interface: ReferenceSequenceFile

Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file.

Specified by:

reset in interface ReferenceSequenceFile

isIndexed

public boolean isIndexed()

Specified by:

isIndexed in interface ReferenceSequenceFile

Returns:

true if getSequence and getSubsequenceAt methods are allowed.

getSequence

public ReferenceSequence getSequence(java.lang.String contig)

Description copied from interface: ReferenceSequenceFile

Retrieves the complete sequence described by this contig.

Specified by:

getSequence in interface ReferenceSequenceFile

Parameters:

contig - contig whose data should be returned.

Returns:

The full sequence associated with this contig.

getSubsequenceAt

public ReferenceSequence getSubsequenceAt(java.lang.String contig,
                                          long start,
                                          long stop)

Description copied from interface: ReferenceSequenceFile

Gets the subsequence of the contig in the range [start,stop]

Specified by:

getSubsequenceAt in interface ReferenceSequenceFile

Parameters:

contig - Contig whose subsequence to retrieve.

start - inclusive, 1-based start of region.

stop - inclusive, 1-based stop of region.

Returns:

The partial reference sequence associated with this range.

close

public void close()
           throws java.io.IOException

Specified by:

close in interface ReferenceSequenceFile

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.io.IOException

loadSequenceDictionary

protected SAMSequenceDictionary loadSequenceDictionary()
                                                throws ngs.ErrorMsg

Throws:

ngs.ErrorMsg