X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ccode.h;fp=ccode.h;h=6322292c12534fc44838255ed6490da4292bbf46;hb=40873e9a7e12d248ebb86e75ca96238c7e7b9701;hp=cced0b7d404b4145a437b677f37fa869bb8abb3f;hpb=952a85d59a12e664f5efa6d01681be189e4fff9c;p=mothur.git

diff --git a/ccode.h b/ccode.h
index cced0b7..6322292 100644
--- a/ccode.h
+++ b/ccode.h
@@ -45,21 +45,42 @@ class Ccode : public Chimera {
 		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();