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/*******************************************************************************
* $Id: MaskedMemHash.cpp,v 1.3 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 "libMems/MaskedMemHash.h"
#include <list>
using namespace std;
using namespace genome;
namespace mems {
MaskedMemHash::MaskedMemHash(){
seq_mask = 0;
}
MaskedMemHash::MaskedMemHash(const MaskedMemHash& mh) : MemHash(mh){
*this = mh;
}
MaskedMemHash& MaskedMemHash::operator=( const MaskedMemHash& mh ){
seq_mask = mh.seq_mask;
return *this;
}
MaskedMemHash* MaskedMemHash::Clone() const{
return new MaskedMemHash(*this);
}
boolean MaskedMemHash::HashMatch(list<idmer>& match_list){
//check that there is at least one forward component
match_list.sort(&idmer_id_lessthan);
// initialize the hash entry
MatchHashEntry mhe = MatchHashEntry(seq_count, GetSar(0)->SeedLength());
mhe.SetLength(GetSar(0)->SeedLength());
//Fill in the new Match and set direction parity if needed.
list<idmer>::iterator iter = match_list.begin();
for(; iter != match_list.end(); iter++)
mhe.SetStart(iter->id, iter->position + 1);
SetDirection(mhe);
mhe.CalculateOffset();
uint64 match_number = 0;
// compute "MatchNumber"
for( uint seqI = 0; seqI < mhe.SeqCount(); seqI++ )
{
match_number <<= 1;
if( mhe.Start(seqI) != NO_MATCH )
match_number |= 1;
}
if( seq_mask == 0 || match_number == seq_mask )
AddHashEntry(mhe);
return true;
}
} // namespace mems
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