libMems/DNAFileSML.cpp

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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(){
}

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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