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/*****************************************************************************
* *
* PLAST : Parallel Local Alignment Search Tool *
* Version 2.3, released November 2015 *
* Copyright (c) 2009-2015 Inria-Cnrs-Ens *
* *
* PLAST is free software; you can redistribute it and/or modify it under *
* the Affero GPL ver 3 License, that is compatible with the GNU General *
* Public License *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* Affero GPL ver 3 License for more details. *
*****************************************************************************/
/** \file AbstractHitIterator.hpp
* \brief Abstract implementation of IHitIterator interface
* \date 07/11/2011
* \author edrezen
*/
#ifndef _ABSTRACT_HITITERATOR_HPP_
#define _ABSTRACT_HITITERATOR_HPP_
/********************************************************************************/
#include <algo/hits/api/IHitIterator.hpp>
#include <stdio.h>
/********************************************************************************/
namespace algo {
namespace hits {
/** \brief Abstract implementations for IHitIterator interface. */
namespace common {
/********************************************************************************/
/** \brief Abstract implementation of IHitIterator interface
*
* This class implements a few methods of the IHitIterator interface and is used
* as a base class for complete implementations.
*
* In particular, AbstractHitIterator manages:
* - a list of IHitIterator instance for splitting process
* - informative methods (getInputHitsNumber(), getOutputHitsNumber()) according to the split scheme
* - default implementation of the update() method
*
* The class is still abstract; complete implementations have to tell how to effectively
* iterate hits (ie. have to implement the iterate() method).
*/
class AbstractHitIterator : public IHitIterator
{
public:
/** Constructor.
*/
AbstractHitIterator ()
: _inputHitsNumber(0), _outputHitsNumber(0),
_maxHitsPerIteration (1000*1000),
_totalTime(0) {}
/** Destructor. */
virtual ~AbstractHitIterator ()
{
for (size_t i=0; i<_splitIterators.size(); i++) { _splitIterators[i]->forget(); }
}
/** \copydoc IHitIterator::getInputHitsNumber */
u_int64_t getInputHitsNumber ();
/** \copydoc IHitIterator::getOutputHitsNumber */
u_int64_t getOutputHitsNumber ();
/** \copydoc IHitIterator::update
* This implementation just forwards the notification.
*/
void update (dp::EventInfo* evt, dp::ISubject* subject)
{
/** We forward the event to potential clients. */
if (this != subject) { notify (evt); }
}
/** \copydoc IHitIterator::getProperties */
dp::IProperties* getProperties ();
protected:
/** Number of incoming hits. */
u_int64_t _inputHitsNumber;
/** Number of outcoming hits. */
u_int64_t _outputHitsNumber;
/** Set referenced split instances (ensure use/forget and observer managements).
* Should be used to link split instances to the instance from which they have
* been split.
* \param[in] split : the split instances to be linked to the current instance.
*/
void setSplitIterators (const std::vector<IHitIterator*>& split);
/** Set of split IHitIterator instances linked to the current instance. */
std::vector<IHitIterator*> _splitIterators;
/** Threshold for controlling memory usage. */
u_int32_t _maxHitsPerIteration;
/** Statistics. */
u_int32_t _totalTime;
};
/********************************************************************************/
}}} /* end of namespaces. */
/********************************************************************************/
#endif /* _ABSTRACT_HITITERATOR_HPP_ */
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