ngs.itf.AlignmentIteratorItf Maven / Gradle / Ivy
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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.itf;
import ngs.ErrorMsg;
import ngs.Fragment;
import ngs.Alignment;
import ngs.AlignmentIterator;
/*==========================================================================
* AlignmentIteratorItf
* represents an alignment between a Fragment and Reference sub-sequence
* provides a path to Read and mate Alignment
*/
class AlignmentIteratorItf
extends AlignmentItf
implements AlignmentIterator
{
/*******************************
* AlignmentIterator Interface *
*******************************/
/* nextAlignment
* advance to first alignment on initial invocation
* advance to next Alignment subsequently
* returns false if no more Alignments are available.
* throws exception if more Alignments should be available,
* but could not be accessed.
*/
public boolean nextAlignment ()
throws ErrorMsg
{
return this . NextAlignment ( self );
}
/***************************************
* AlignmentIteratorItf Implementation *
***************************************/
// constructors
AlignmentIteratorItf ( long ref )
{
super ( ref );
}
AlignmentIteratorItf ( AlignmentIterator obj )
throws ErrorMsg
{
super ( 0 );
try
{
AlignmentIteratorItf ref = ( AlignmentIteratorItf ) obj;
this . self = ref . duplicate ();
}
catch ( Exception x )
{
throw new ErrorMsg ( x . toString () );
}
}
// native interface
private native boolean NextAlignment ( long self )
throws ErrorMsg;
}