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/*******************************************************************************
* $Id: RepeatHash.cpp,v 1.13 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/RepeatHash.h"
#include <list>
using namespace std;
using namespace genome;
namespace mems {
RepeatHash* RepeatHash::Clone() const{
return new RepeatHash(*this);
}
boolean RepeatHash::CreateMatches(){
if(seq_count == 1){
MatchFinder::FindMatchSeeds();
return true;
}
return false;
}
boolean RepeatHash::EnumerateMatches( IdmerList& match_list ){
return HashMatch(match_list);
}
//why have separate hash tables?
// RepeatHashEntries use GENETICIST coordinates. They start at 1, not 0.
boolean RepeatHash::HashMatch(IdmerList& match_list){
//check that there is at least one forward component
match_list.sort(&idmer_position_lessthan);
// initialize the hash entry
MatchHashEntry mhe = MatchHashEntry( match_list.size(), GetSar(0)->SeedLength());
mhe.SetLength( GetSar(0)->SeedLength() );
//Fill in the new Match and set direction parity if needed.
IdmerList::iterator iter = match_list.begin();
uint32 repeatI = 0;
for(; iter != match_list.end(); iter++)
mhe.SetStart(repeatI++, iter->position + 1);
SetDirection( mhe );
mhe.CalculateOffset();
if(mhe.Multiplicity() < 2){
cout << "red flag " << mhe << "\n";
}else{
AddHashEntry(mhe);
}
return true;
}
} // namespace mems
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