/*
Copyright 2010 Daniel Zerbino (zerbino@ebi.ac.uk)

    This file is part of Velvet.

    Velvet 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 2 of the License, or
    (at your option) any later version.

    Velvet 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 Velvet; if not, write to the Free Software
    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA

*/
#ifndef _KMEROCCURENCETABLE_H_
#define _KMEROCCURENCETABLE_H_

// Table operations
KmerOccurenceTable * newKmerOccurenceTable(short int accelerationBits, int wordLength);

void allocateKmerOccurences(IDnum kmerCount, KmerOccurenceTable * table);

void recordKmerOccurence(Kmer * kmer, IDnum nodeID, Coordinate position, KmerOccurenceTable * table);

void sortKmerOccurenceTable(KmerOccurenceTable * table);

KmerOccurence *findKmerInKmerOccurenceTable(Kmer * kmer,
						     KmerOccurenceTable *
						     table);


void destroyKmerOccurenceTable(KmerOccurenceTable * kmerTable);

// Node operations
KmerOccurence * getNextKmerOccurence(KmerOccurence * current);
IDnum getKmerOccurenceNodeID(KmerOccurence * occurence);
Coordinate getKmerOccurencePosition(KmerOccurence * occurence);
#endif