vector<linePair*> templateLines;
vector<Sequence*> querySeqs;
vector<Sequence*> templateSeqs;
+ vector< map<int, int> > spotMap;
+ map<int, int>::iterator it;
- vector<int> windows;
- vector< vector<Sequence*> > closest; //closest[0] is a vector of sequence at are closest to queryseqs[0]...
+ vector< vector<int> > windows; //windows[0] is the vector of window breaks for querySeqs[0]
+ vector<int> windowSizes; //windowSizes[0] is the size of the windows for querySeqs[0]
+ vector< map<int, int> > trim; //trim[0] is the map containing the starting and ending positions for querySeqs[0] set of seqs
+ vector< vector<SeqDist> > closest; //closest[0] is a vector of sequence at are closest to queryseqs[0]...
vector< vector<float> > averageRef; //averageRef[0] is the average distance at each window for the references for querySeqs[0]
vector< vector<float> > averageQuery; //averageQuery[0] is the average distance at each winow for the query for querySeqs[0]
+ vector< vector<float> > sumRef; //sumRef[0] is the sum of distances at each window for the references for querySeqs[0]
+ vector< vector<float> > sumSquaredRef; //sumSquaredRef[0] is the sum of squared distances at each window for the references for querySeqs[0]
+ vector< vector<float> > sumQuery; //sumQuery[0] is the sum of distances at each window for the comparison of query to references for querySeqs[0]
+ vector< vector<float> > sumSquaredQuery; //sumSquaredQuery[0] is the sum of squared distances at each window for the comparison of query to references for querySeqs[0]
+ vector< vector<float> > varRef; //varRef[0] is the variance among references seqs at each window for querySeqs[0]
+ vector< vector<float> > varQuery; //varQuery[0] is the variance among references and querySeqs[0] at each window
+ vector< vector<float> > sdRef; //sdRef[0] is the standard deviation of references seqs at each window for querySeqs[0]
+ vector< vector<float> > sdQuery; //sdQuery[0] is the standard deviation of references and querySeqs[0] at each window
+ vector< vector<float> > anova; //anova[0] is the vector of anova scores for each window for querySeqs[0]
+ vector<int> refCombo; //refCombo[0] is the number of reference sequences combinations for querySeqs[0]
+ vector< vector<bool> > isChimericConfidence; //isChimericConfidence[0] indicates whether querySeqs[0] is chimeric at a given window according to the confidence limits
+ vector< vector<bool> > isChimericTStudent; //isChimericConfidence[0] indicates whether querySeqs[0] is chimeric at a given window according to the confidence limits
+ vector< vector<bool> > isChimericANOVA; //isChimericConfidence[0] indicates whether querySeqs[0] is chimeric at a given window according to the confidence limits
- vector< vector<Sequence*> > findClosest(int, int, int);
- void removeBadReferenceSeqs(vector<Sequence*>&, int); //removes sequences from closest that are to different of too similar to eachother.
- void trimSequences();
- vector<int> findWindows();
- vector<float> getAverageRef(vector<Sequence*>);
- vector<float> getAverageQuery (vector<Sequence*>, int);
-
+ vector< vector<SeqDist> > findClosest(int, int, int);
+ void removeBadReferenceSeqs(vector<SeqDist>&, int); //removes sequences from closest that are to different of too similar to eachother.
+ void trimSequences(int);
+ vector<int> findWindows(int);
+ void getAverageRef(vector<SeqDist>, int); //fills sumRef[i], averageRef[i], sumSquaredRef[i] and refCombo[i].
+ void getAverageQuery (vector<SeqDist>, int); //fills sumQuery[i], averageQuery[i], sumSquaredQuery[i].
+ void findVarianceRef (int); //fills varRef[i] and sdRef[i] also sets minimum error rate to 0.001 to avoid divide by 0.
+ void findVarianceQuery (int); //fills varQuery[i] and sdQuery[i]
+ void determineChimeras (int); //fills anova, isChimericConfidence[i], isChimericTStudent[i] and isChimericANOVA[i].
int getDiff(string, string); //return number of mismatched bases, a gap to base is not counted as a mismatch
+ float getT(int);
+ float getF(int);
void createProcessesClosest();