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/*******************************************************************************
* $Id: PairwiseMatchFinder.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/PairwiseMatchFinder.h"
#include <list>
using namespace std;
using namespace genome;
namespace mems {
PairwiseMatchFinder::PairwiseMatchFinder(){
}
PairwiseMatchFinder::~PairwiseMatchFinder(){
}
PairwiseMatchFinder::PairwiseMatchFinder(const PairwiseMatchFinder& mh) : MemHash(mh){
}
PairwiseMatchFinder* PairwiseMatchFinder::Clone() const{
return new PairwiseMatchFinder(*this);
}
// enumerate out every pairwise match
boolean PairwiseMatchFinder::EnumerateMatches( IdmerList& match_list ){
match_list.sort(&idmer_id_lessthan);
IdmerList::iterator iter = match_list.begin();
IdmerList::iterator iter2 = match_list.begin();
uint cur_id_count = 1;
IdmerList unique_list;
// identify all of the unique seeds and add them to unique_list
while(iter2 != match_list.end()){
++iter2;
if(iter2 == match_list.end() || iter->id != iter2->id){
if( cur_id_count == 1 )
unique_list.push_back( *iter );
else
cur_id_count = 1;
}else
cur_id_count++;
++iter;
}
// hash each pair of unique seeds
boolean success = true;
for( iter = unique_list.begin(); iter != unique_list.end(); ++iter )
{
for( iter2 = iter; iter2 != unique_list.end(); ++iter2 )
{
if( iter == iter2 )
continue;
IdmerList hash_list;
hash_list.push_back( *iter );
hash_list.push_back( *iter2 );
success = success && HashMatch(hash_list);
}
}
return success;
}
} // namespace mems
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