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/*******************************************************************************
* $Id: MemorySML.h,v 1.7 2004/03/01 02:40:08 darling Exp $
* This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file.
* This file is licensed under the GPL.
* Please see the file called COPYING for licensing details.
* **************
******************************************************************************/
#ifndef _MemorySML_h_
#define _MemorySML_h_
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnSequence.h"
#include "libMems/SortedMerList.h"
namespace mems {
/** The MemorySML is an implementation of sorted mer lists which creates and
* stores the sorted mer list entirely in memory. A MemorySML consumes
* roughly 32 + alpha_bits bits of memory per character in the sequences.
* For unambiguous DNA sequences 4.25 bytes per base are required.
*/
class MemorySML : public SortedMerList
{
public:
/**
* Create an empty MemorySML
* Creates an empty MemorySML with the supplied translation
* table and alphabet bit size. Defaults to DNA settings
* @param table The array used to translate characters into binary code
* @param alpha_bits The number of bits each character consumes in binary
*/
MemorySML(const uint8* table = SortedMerList::BasicDNATable(), const uint32 alpha_bits = DNA_ALPHA_BITS);
MemorySML(const MemorySML& msa);
MemorySML& operator=(const MemorySML& msa );
MemorySML* Clone() const;
virtual void Clear();
virtual void Create(const genome::gnSequence& seq, const uint64 seed);
virtual boolean Read(std::vector<bmer>& readVector, gnSeqI size, gnSeqI offset = 0);
virtual void Merge(SortedMerList& sa, SortedMerList& sa2);
virtual bmer operator[](gnSeqI index);
protected:
// virtual void FillSML(const gnSeqI seq_len, vector<gnSeqI>& sml_array);
std::vector<smlSeqI_t> positions;
};
}
#endif //_MemorySML_h_
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