libMems/DNAMemorySML.h

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00001 /*******************************************************************************
00002  * $Id: DNAMemorySML.h,v 1.3 2004/03/01 02:40:08 darling Exp $
00003  * This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file.
00004  * This file is licensed under the GPL.
00005  * Please see the file called COPYING for licensing details.
00006  * **************
00007  ******************************************************************************/
00008 
00009 #ifndef _DNAMemorySML_h_
00010 #define _DNAMemorySML_h_
00011 
00012 #ifdef HAVE_CONFIG_H
00013 #include "config.h"
00014 #endif
00015 
00016 #include "libGenome/gnSequence.h"
00017 #include "libMems/MemorySML.h"
00018 
00019 namespace mems {
00020 
00027 class DNAMemorySML : public MemorySML
00028 {
00029 public:
00037         DNAMemorySML(const uint8* table = SortedMerList::BasicDNATable(), const uint32 alpha_bits = DNA_ALPHA_BITS);
00038         DNAMemorySML(const DNAMemorySML& msa);
00039         DNAMemorySML(const SortedMerList& sa);
00040         DNAMemorySML& operator=(const DNAMemorySML& msa );
00041         DNAMemorySML* Clone() const;
00042         
00043         
00044         virtual uint64 GetMer(gnSeqI offset) const;
00045         virtual uint64 GetSeedMer( gnSeqI offset ) const;
00046         
00047 protected:
00048 
00049         virtual void FillSML(const genome::gnSequence& seq, std::vector<bmer>& sml_array);
00050 
00051 };
00052 
00053 }
00054 
00055 #endif   //_DNAMemorySML_h_

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