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/*
* Ray -- Parallel genome assemblies for parallel DNA sequencing
* Copyright (C) 2013 Sébastien Boisvert
*
* http://DeNovoAssembler.SourceForge.Net/
*
* This program 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, version 3 of the 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
* GNU General Public License for more details.
*
* You have received a copy of the GNU General Public License
* along with this program (gpl-3.0.txt).
* see <http://www.gnu.org/licenses/>
*/
#ifndef _SeedFilteringWorkflow_h
#define _SeedFilteringWorkflow_h
#include <code/SeedingData/GraphPath.h>
#include <code/Mock/Parameters.h>
#include <RayPlatform/core/ComputeCore.h>
#include <RayPlatform/scheduling/TaskCreator.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <vector>
using namespace std;
/**
* This is the workflow that will be deposited on the
* virtual processor.
*
* \author Sébastien Boisvert
*/
class SeedFilteringWorkflow: public TaskCreator {
ComputeCore*m_core;
int m_seedIndex;
Parameters * m_parameters;
vector<GraphPath>*m_seeds;
vector<bool> m_states;
int m_finished;
int m_rank;
int m_period;
/* TODO: maybe this should be in the TaskCreator */
VirtualCommunicator * m_virtualCommunicator;
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH;
public:
/*
* Methods to implement for the TaskCreator interface.
*
* The TaskCreator stack is used in the handler
* RAY_SLAVE_MODE_FILTER_SEEDS.
*/
/** initialize the whole thing */
void initializeMethod();
/** finalize the whole thing */
void finalizeMethod();
/** has an unassigned task left to compute */
bool hasUnassignedTask();
/** assign the next task to a worker and return this worker */
Worker*assignNextTask();
/** get the result of a worker */
void processWorkerResult(Worker*worker);
/** destroy a worker */
void destroyWorker(Worker*worker);
void initialize(vector<GraphPath>*seeds, VirtualCommunicator*virtualCommunicator,
VirtualProcessor * virtualProcessor, ComputeCore * core,
Parameters * parameters, MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT,
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE,
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH
);
};
#endif
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