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/*
Ray
Copyright (C) 2011, 2012 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 _GridTable
#define _GridTable
#include "Vertex.h"
#include <code/KmerAcademyBuilder/Kmer.h>
#include <code/Mock/Parameters.h>
#include <RayPlatform/structures/MyHashTable.h>
#include <RayPlatform/memory/MyAllocator.h>
/**
* The GridTable stores all the k-mers for the graph.
* Low-coverage (covered once) are not stored here at all.
* The underlying data structure is a MyHashTable.
* \author Sébastien Boisvert
*/
class GridTable{
MyHashTable<Kmer,Vertex> m_hashTable;
Parameters*m_parameters;
LargeCount m_size;
bool m_inserted;
LargeCount m_findOperations;
/** verbosity */
bool m_verbose;
public:
void constructor(Rank rank,Parameters*a);
LargeCount size();
Vertex*find(Kmer*key);
Vertex*insert(Kmer*key);
bool inserted();
void addRead(Kmer*a,ReadAnnotation*e);
ReadAnnotation*getReads(Kmer*a);
void addDirection(Kmer*a,Direction*d);
vector<Direction> getDirections(Kmer*a);
void clearDirections(Kmer*a);
void buildData(Parameters*a);
bool isAssembled(Kmer*a);
bool isAssembledByGreaterRank(Kmer*a,Rank origin);
MyHashTable<Kmer,Vertex>*getHashTable();
void printStatistics();
void completeResizing();
void printStatus();
};
#endif
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