+ Sequence* bestfit; //closest match to query in template
- 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> > windowsForeachQuery; // windowsForeachQuery[0] is a vector containing the starting spot in queryseqs[0] aligned sequence for each window.
+ 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
//this is needed so you can move by bases and not just spots in the alignment
- vector<int> windowSizes; //windowSizes[0] = window size of querySeqs[0]
+ int windowSizes; //windowSizes = window size of query
vector<int> windowSizesTemplate; //windowSizesTemplate[0] = window size of templateSeqs[0]
vector<int> windowSizesTemplate; //windowSizesTemplate[0] = window size of templateSeqs[0]
- vector< map<int, int> > trimmed; //trimmed[0] = start and stop of trimmed sequences for querySeqs[0]
+ map<int, int> trimmed; //trimmed = start and stop of trimmed sequences for query
map<int, int>::iterator it;
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> 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<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<quanMember> > 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...
- vector< set<int> > h;
+ 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...
+ set<int> h;
+ string mergedFilterString;
-
- vector<float> readFreq();
vector< vector<float> > readQuantiles();
vector< vector<float> > readQuantiles();
- vector<Sequence*> findPairs(int, int);
+ vector<float> readFreq();
+ Sequence* findPairs(Sequence*);
- void createProcessesSpots();
- void createProcessesPairs();
- void createProcesses();
void createProcessesQuan();
void createProcessesQuan();
-
- vector<float> makeCompliant; //used by decalc->getQuantiles so pintail and mallard can use same function, it contains the highest de value for each seq in the template