- 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;
+ vector< map<int, int> > trimmed; //trimmed[0] = start and stop of trimmed sequences for querySeqs[0]
+ map<int, int>::iterator it;
+
+ vector< vector<float> > Qav; //Qav[0] is the vector of average variablility for queryseqs[0]...
+ vector<float> seqCoef; //seqCoef[0] is the coeff for queryseqs[0]...
+ vector<float> DE; //DE[0] is the deviaation for queryseqs[0]...
+ 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< set<int> > h;
+
+
+ vector<float> readFreq();
+ vector< vector<float> > readQuantiles();
+ vector<Sequence> findPairs(int, int);
+
+ void createProcessesSpots();
+ void createProcesses();
+ void createProcessesQuan();