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/*******************************************************************************
* $Id: DNAFileSML.cpp,v 1.4 2004/03/01 02:40:08 darling Exp $
* This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file.
* Please see the file called COPYING for licensing, copying, and modification
* Please see the file called COPYING for licensing details.
* **************
******************************************************************************/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnSequence.h"
#include "libGenome/gnFilter.h"
#include "libMems/DNAFileSML.h"
using namespace std;
using namespace genome;
namespace mems {
DNAFileSML::DNAFileSML() : FileSML(){
FileSML::header.version = FormatVersion();
}
DNAFileSML::DNAFileSML(const string& fname, const uint8* table, const uint32 alpha_bits){
header.alphabet_bits = alpha_bits;
memcpy(header.translation_table, table, UINT8_MAX);
filename = fname;
header.version = FormatVersion();
}
DNAFileSML& DNAFileSML::operator=(const DNAFileSML& msa ){
FileSML::operator=(msa);
return *this;
}
DNAFileSML* DNAFileSML::Clone() const{
DNAFileSML *bdsa = new DNAFileSML();
(*bdsa) = *this;
return bdsa;
}
uint64 DNAFileSML::GetNeededMemory(gnSeqI len){
uint64 neededmem = (len * FileSML::header.alphabet_bits) / 8;
//forward and reverse copies of the sequence
neededmem += len * 2;
neededmem += sizeof(bmer) * len;
return neededmem;
}
uint32 DNAFileSML::CalculateMaxMerSize() const{
return 62 / header.alphabet_bits;
}
uint64 DNAFileSML::GetMer(gnSeqI position) const{
return GetDnaMer( position );
}
uint64 DNAFileSML::GetSeedMer( gnSeqI offset ) const{
return GetDnaSeedMer( offset );
}
void DNAFileSML::FillSML(const gnSequence& seq, vector<bmer>& sml_array)
{
FillDnaSML(seq, sml_array);
}
} // namespace mems
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