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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
package ngs;
/**
* Represents a reference sequence standalone object
*/
public interface ReferenceSequence
{
/**
* getCanonicalName
* @return the accessioned name of reference, e.g. "NC_000001.11"
* @throws ErrorMsg if no cannonical name found
*/
String getCanonicalName ()
throws ErrorMsg;
/**
* getIsCircular
* @return true if reference is circular
* @throws ErrorMsg if cannot detect if reference is circular
*/
boolean getIsCircular ()
throws ErrorMsg;
/**
* getLength
* @return the length of the reference sequence
* @throws ErrorMsg if length cannot be detected
*/
long getLength ()
throws ErrorMsg;
/**
* getReferenceBases
* @param offset is zero-based and non-negative
* @return sub-sequence bases for Reference
* @throws ErrorMsg if no reference-bases found at offset
*/
String getReferenceBases ( long offset )
throws ErrorMsg;
/**
* getReferenceBases
* @param offset is zero-based and non-negative
* @param length must be ≥ 0
* @return sub-sequence bases for Reference
* @throws ErrorMsg if no reference-bases found at offset or lenght invalid
*/
String getReferenceBases ( long offset, long length )
throws ErrorMsg;
/**
* getReferenceChunk
* @param offset is zero-based and non-negative
* @return largest contiguous chunk available of sub-sequence bases for Reference
* <p>
* NB - actual returned sequence may be shorter
* than requested. to obtain all bases available
* in chunk, use a negative "size" value
* </p>
* @throws ErrorMsg if no ReferenceChunk found
*/
String getReferenceChunk ( long offset )
throws ErrorMsg;
/**
* getReferenceChunk
* @param offset is zero-based and non-negative
* @param length must be > 0
* @return largest contiguous chunk available of sub-sequence bases for Reference
* <p>
* NB - actual returned sequence may be shorter
* than requested. to obtain all bases available
* in chunk, use a negative "size" value
* </p>
* @throws ErrorMsg if no ReferenceChunk found
*/
String getReferenceChunk ( long offset, long length )
throws ErrorMsg;
}
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