- map<Sequence*, vector<float> > obsDistance; //maps a query sequence to its observed distance at each window
- map<Sequence*, vector<float> > expectedDistance; //maps a query sequence to its expected distance at each window
- map<Sequence*, vector<float> >::iterator itObsDist;
- map<Sequence*, vector<float> >::iterator itExpDist;
+ vector< vector<float> > obsDistance; //obsDistance[0] is the vector of observed distances for queryseqs[0]...
+ vector< vector<float> > expectedDistance; //expectedDistance[0] is the vector of expected distances for queryseqs[0]...
+ vector<float> deviation; //deviation[0] is the percentage of mismatched pairs over the whole seq between querySeqs[0] and its best match.
+ vector< vector<int> > windows; // windows[0] is a vector containing the starting spot in queryseqs[0] aligned sequence for each window.
+ //this is needed so you can move by bases and not just spots in the alignment
+ vector< map<int, int> > trim; //trim[0] is the start and end position of trimmed querySeqs[0]. Used to find the variability over each sequence window.
+
+ vector<int> windowSizes; //windowSizes[0] = window size of querySeqs[0]