htsjdk.samtools.reference

Interface ReferenceSequenceFile

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable

All Known Implementing Classes:

FastaSequenceFile, IndexedFastaSequenceFile

public interface ReferenceSequenceFile
extends java.io.Closeable

An interface for working with files of reference sequences regardless of the file format being used.

Method Summary

Methods

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()

Method Detail

getSequenceDictionary

SAMSequenceDictionary getSequenceDictionary()

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

Returns:

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

nextSequence

ReferenceSequence nextSequence()

Retrieves the next whole sequences from the file.

Returns:

a ReferenceSequence or null if at the end of the file

reset

void reset()

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

isIndexed

boolean isIndexed()

Returns:

true if getSequence and getSubsequenceAt methods are allowed.

getSequence

ReferenceSequence getSequence(java.lang.String contig)

Retrieves the complete sequence described by this contig.

Parameters:

contig - contig whose data should be returned.

Returns:

The full sequence associated with this contig.

Throws:

java.lang.UnsupportedOperationException - if !sIndexed.

getSubsequenceAt

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

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

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.

Throws:

java.lang.UnsupportedOperationException - if !sIndexed.

toString

java.lang.String toString()

Overrides:

toString in class java.lang.Object

Returns:

Reference name, file name, or something other human-readable representation.

close

void close()
           throws java.io.IOException

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable

Throws:

java.io.IOException