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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 an NGS biological fragment
*/
public interface Fragment
{
/**
* getFragmentId
* @return the unique ID of the fragment
* @throws ErrorMsg upon an error accessing data
*/
String getFragmentId ()
throws ErrorMsg;
/*------------------------------------------------------------------
* fragment details
*/
/**
* getFragmentBases
* @return sequence bases
* @throws ErrorMsg upon an error accessing data
*/
String getFragmentBases ()
throws ErrorMsg;
/**
* getFragmentBases
* @param offset is zero-based and non-negative
* @return sequence bases
* @throws ErrorMsg upon an error accessing data
* @throws IndexOutOfBoundsException upon invalid offset
*/
String getFragmentBases ( long offset )
throws ErrorMsg, IndexOutOfBoundsException;
/**
* getFragmentBases
* @param offset is zero-based and non-negative
* @param length must be ≥ 0
* @return sequence bases
* @throws ErrorMsg upon an error accessing data
* @throws IndexOutOfBoundsException upon invalid offset
*/
String getFragmentBases ( long offset, long length )
throws ErrorMsg, IndexOutOfBoundsException;
/**
* getFragmentQualities using ASCII offset of 33
* @return phred quality values for the whole fragment
* @throws ErrorMsg upon an error accessing data
*/
String getFragmentQualities ()
throws ErrorMsg;
/**
* getFragmentQualities using ASCII offset of 33
* @param offset is zero-based and non-negative
* @return phred quality values
* @throws ErrorMsg upon an error accessing data
* @throws IndexOutOfBoundsException upon invalid offset
*/
String getFragmentQualities ( long offset )
throws ErrorMsg, IndexOutOfBoundsException;
/**
* getFragmentQualities using ASCII offset of 33
* @param offset is zero-based and non-negative
* @param length must be ≥ 0
* @return phred quality values
* @throws ErrorMsg upon an error accessing data
* @throws IndexOutOfBoundsException upon invalid offset/length
*/
String getFragmentQualities ( long offset, long length )
throws ErrorMsg, IndexOutOfBoundsException;
/**
* isPaired
* @return true if fragment has a mate
* @throws ErrorMsg upon an error accessing data
*/
boolean isPaired ()
throws ErrorMsg;
/**
* check to see if Fragment has alignment data (requires interface 1.1)
* @return true if Fragment is aligned
* @throws ErrorMsg if object is invalid or implementation too old
*/
boolean isAligned ()
throws ErrorMsg;
}
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