continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / ccode.h

diff --git a/ccode.h b/ccode.h
index a4860dcb83ee16ddaca43afd6cc4adb4a1973adc..bc1aad8b2b6776c57922ad644e40ef325ea78d4d 100644 (file)
--- a/ccode.h
+++ b/ccode.h
@@ -42,17 +42,51 @@ class Ccode : public Chimera {
                
                
                vector<linePair*> lines;
-               vector<linePair*> templateLines;
                vector<Sequence*> querySeqs;
                vector<Sequence*> templateSeqs;
+               vector< map<int, int> > spotMap;
+               map<int, int>::iterator it;
                
-               vector< vector<Sequence*> > closest;  //bestfit[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 removeSeqs(vector<Sequence*>);  //removes sequences from closest that are to different of too similar to eachother. 
+               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].
                
-               void createProcessesClosest();
+               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();
+               void createProcessesRemoveBad();
+               void createProcessesAverages();
+               void createProcessesVariances();
+               void createProcessesDetermine();
+                               
 };
 
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