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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 _AnnihilationWorker_h
#define _AnnihilationWorker_h
#include "AttributeFetcher.h"
#include "AnnotationFetcher.h"
#include <code/SeedingData/GraphPath.h>
#include <code/Mock/Parameters.h>
#include <code/SeedExtender/Direction.h>
#include <RayPlatform/scheduling/Worker.h>
#include <stack>
#include <vector>
#include <set>
using namespace std;
#include <stdint.h>
/**
* This is a worker that analyze a seed.
*
* \author Sébastien Boisvert
*/
class AnnihilationWorker: public Worker{
AttributeFetcher m_attributeFetcher;
AnnotationFetcher m_annotationFetcher;
uint64_t m_identifier; // TODO this should be in Worker because it's always there anyway
bool m_done; // TODO this should be in Worker because it's always there anyway
GraphPath * m_seed;
VirtualCommunicator * m_virtualCommunicator; // TODO this should be in Worker because it's always there anyway
Parameters * m_parameters;
Kmer m_parent;
Kmer m_grandparent;
Kmer m_child;
Kmer m_grandchild;
int m_step;
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH;
int STEP_CHECK_LENGTH;
int STEP_CHECK_DEAD_END_ON_THE_LEFT;
int STEP_CHECK_DEAD_END_ON_THE_RIGHT;
int STEP_CHECK_BUBBLE_PATTERNS;
int STEP_FETCH_FIRST_PARENT;
int STEP_FETCH_SECOND_PARENT;
int STEP_DOWNLOAD_ORIGINAL_ANNOTATIONS;
int STEP_GET_SEED_SEQUENCE_NOW;
bool m_queryWasSent;
Rank m_rank;
RingAllocator*m_outboxAllocator;
bool m_startedToCheckDeadEndOnTheLeft;
bool m_startedToCheckDeadEndOnTheRight;
stack<int> m_depths;
stack<Kmer> m_vertices;
int m_maximumAllowedDepth;
int m_actualMaximumDepth;
int m_maximumDepthForExploration;
bool m_valid;
set<Kmer> m_visited;
bool m_searchIsStarted;
int DIRECTION_PARENTS;
int DIRECTION_CHILDREN;
bool m_fetchedFirstParent;
bool m_fetchedSecondParent;
bool m_fetchedFirstChild;
bool m_fetchedSecondChild;
vector<Direction> m_leftDirections;
vector<Direction> m_rightDirections;
bool m_fetchedGrandparentDirections;
bool m_fetchedGrandchildDirections;
bool m_fetchedGrandparentReverseDirections;
bool m_fetchedGrandchildReverseDirections;
bool m_isPerfectBubble;
// private methods
bool checkDeadEndOnTheLeft();
bool checkDeadEndOnTheRight();
bool searchGraphForNiceThings(int direction);
bool checkBubblePatterns();
bool getOtherBestParent(Kmer*kmer);
bool getOtherBestChild(Kmer*kmer);
bool getBestChild(Kmer*kmer);
bool getBestParent(Kmer*kmer);
public:
void work();
bool isDone();
WorkerHandle getWorkerIdentifier();
void initialize(uint64_t identifier, GraphPath*seed, Parameters * parameters,
VirtualCommunicator * virtualCommunicator,
RingAllocator * outboxAllocator,
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT,
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE, MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH
);
bool isValid();
};
#endif
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