ngs.itf.ReadGroupItf 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.ReadGroup;
import ngs.Read;
import ngs.ReadIterator;
import ngs.Statistics;
/*==========================================================================
* ReadGroupItf
* represents an NGS-capable object with a group of Reads
*/
class ReadGroupItf
extends Refcount
implements ReadGroup
{
/***********************
* ReadGroup Interface *
***********************/
/* getName
* returns the simple name of the read group
*/
public String getName ()
throws ErrorMsg
{
return this . GetName ( self );
}
/*------------------------------------------------------------------
* READS
* [ support for reads has been removed ]
*/
/* getRead
* returns an individual Read
* throws ErrorMsg if Read does not exist
* or is not part of this ReadGroup
*/
/*
public Read getRead ( String readId )
throws ErrorMsg
{
long ref = this . GetRead ( self, readId );
try
{
return new ReadItf ( ref );
}
catch ( Exception x )
{
this . release ( ref );
throw new ErrorMsg ( x . toString () );
}
}
*/
/* ReadCategory
* see Read for category definitions
*/
/* getReads
* returns an iterator of all contained machine Reads
*/
/*
public ReadIterator getReads ( int categories )
throws ErrorMsg
{
long ref = this . GetReads ( self, categories );
try
{
return new ReadIteratorItf ( ref );
}
catch ( Exception x )
{
this . release ( ref );
throw new ErrorMsg ( x . toString () );
}
}
*/
public Statistics getStatistics ()
throws ErrorMsg
{
long ref = this . GetStatistics ( self );
try
{
return new StatisticsItf ( ref );
}
catch ( Exception x )
{
this . release ( ref );
throw new ErrorMsg ( x . toString () );
}
}
/************************************
* ReadGroupItf Implementation *
************************************/
// constructors
ReadGroupItf ( long ref )
{
super ( ref );
}
ReadGroupItf ( ReadGroup obj )
throws ErrorMsg
{
super ( 0 );
try
{
ReadGroupItf ref = ( ReadGroupItf ) obj;
this . self = ref . duplicate ();
}
catch ( Exception x )
{
throw new ErrorMsg ( x . toString () );
}
}
// native interface
private native String GetName ( long self )
throws ErrorMsg;
/*
private native long GetRead ( long self, String readId )
throws ErrorMsg;
private native long GetReads ( long self, int categories )
throws ErrorMsg;
*/
private native long GetStatistics ( long self )
throws ErrorMsg;
}