AbstractAlignerSafe.hpp

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/*******************************************************************************
 *
 * Copyright (c) 2010-2015   Edans Sandes
 *
 * This file is part of MASA-Core.
 * 
 * MASA-Core is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * MASA-Core 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
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with MASA-Core.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/

#ifndef ABSTRACTALIGNERSAFE_HPP_
#define ABSTRACTALIGNERSAFE_HPP_

#include "AbstractAligner.hpp"
#include <pthread.h>
#include <queue>
using namespace std;


struct dispatch_job_t {
        enum dispatch_type_e {JOB_SCORE} type;
        union dispatch_params_t {
                struct params_score_t {
                        score_t score;
                        int bx;
                        int by;
                } params_score;
        } dispatch_params;
};

/** @brief A thread-safe AbstractAligner extension.
 *
 * The current MASA implementation is not thread-safe. So, if an Aligner
 * executes simultaneous threads, the dispatch methods may generate an
 * inconsistent state leading to segmentation faults. To avoid this behavior,
 * the Aligner must extend the AbstractAlignerSafe class in order to
 * serialize the dispatch calls.
 *
 * There are two serialization strategies.
 *
 * <ul>
 *  <li>Serialize by Mutex: the class uses mutex to lock simultaneous threads.
 *      The threads are locked until no other thread is dispatching.
 *  <li>Serialize by Queue: the class enqueue all dispatch executions and a
 *      consumer thread dispatches the requisitions to the MASA engine. The
 *      threads are only locked during the enqueue process. By now, only the
 *      dispatchScore function is queued. To enable this feature, use
 *      the createDispatcherQueue and destroyDispatcherQueue in the
 *      alignPartition method.
 * </ul>
 */
class AbstractAlignerSafe : public AbstractAligner {
public:
        AbstractAlignerSafe();
        virtual ~AbstractAlignerSafe();

        virtual void dispatchColumn(int j, const cell_t* buffer, int len);
        virtual void dispatchRow(int i, const cell_t* buffer, int len);
        virtual void dispatchScore(score_t score, int bx=-1, int by=-1);

protected:
        void createDispatcherQueue();
        void destroyDispatcherQueue();

private:
        pthread_t thread;
        pthread_mutex_t mutex;
        pthread_cond_t condition;
        bool dispatcherQueueActive;
        queue<dispatch_job_t> dispatcherQueue;

        static void *staticFunctionThread(void *arg);
        void executeLoop();
};

#endif /* ABSTRACTALIGNERSAFE_HPP_ */