vector<linePair*> lines;
vector<Sequence*> querySeqs;
vector<Sequence*> templateSeqs;
+ vector< map<int, int> > spotMap;
vector< vector<data_struct> > chimeraResults;
vector<string> chimeraFlags;
string fastafile, templateFile;
Sequence* getSequence(string); //find sequence from name
-
-
+ void printBlock(data_struct, ostream&, int i);
};
/************************************************************************/