+ vector<float> obsDistance; //obsDistance is the vector of observed distances for query
+ vector<float> expectedDistance; //expectedDistance is the vector of expected distances for query
+ float deviation; //deviation is the percentage of mismatched pairs over the whole seq between query and its best match.
+ vector<int> windowsForeachQuery; // windowsForeachQuery is a vector containing the starting spot in query aligned sequence for each window.
+ //this is needed so you can move by bases and not just spots in the alignment
+
+ int windowSizes; //windowSizes = window size of query
+ vector<int> windowSizesTemplate; //windowSizesTemplate[0] = window size of templateSeqs[0]
- vector<float> averageProbability; //Qav
- map<Sequence*, float> seqCoef; //maps a sequence to its coefficient
- map<Sequence*, float> DE; //maps a sequence to its deviation
- map<Sequence*, float>::iterator itCoef;
+ map<int, int> trimmed; //trimmed = start and stop of trimmed sequences for query
+ map<int, int>::iterator it;
- vector<Sequence*> readSeqs(string);
- vector<float> findQav(vector<float>);
- vector<float> calcFreq(vector<Sequence*>);
- map<Sequence*, float> getCoef(vector<float>);
+ vector<float> Qav; //Qav is the vector of average variablility for query
+ float seqCoef; //seqCoef is the coeff for query
+ float DE; //DE is the deviaation for query
+ vector<float> probabilityProfile;
+ vector< vector<float> > quantiles; //quantiles[0] is the vector of deviations with ceiling score of 1, quantiles[1] is the vector of deviations with ceiling score of 2...
+ vector< vector<float> > quantilesMembers; //quantiles[0] is the vector of deviations with ceiling score of 1, quantiles[1] is the vector of deviations with ceiling score of 2...