#include "chimera.h"
#include "kmer.hpp"
#include "kmerdb.hpp"
-#include "database.hpp"
+#include "alignmentdb.h"
/***********************************************************/
//This class was created using the algorythms described in
vector<linePair*> lines;
vector<Sequence*> querySeqs;
- Database* templateDB;
+ AlignmentDB* templateDB;
Kmer* kmer;
vector< vector<sim> > IS; //IS[0] is the vector of IS values for each window for querySeqs[0]