-
- vector< vector<sim> > IS; //IS[0] is the vector of IS values for each window for querySeqs[0]
- float chimeraCutoff;
-
-
- //map<string, vector< map<int, int> > >:: iterator it;
- //map<int, int>::iterator it2;
-
- vector<Sequence> closest; //closest[0] is the closest overall seq to querySeqs[0].
-
- string fastafile, templateFile;
+ Sequence closest; //closest is the closest overall seq to query
+
+ vector<sim> IS; //IS is the vector of IS values for each window for query
+ string fastafile;