#include "dist.h"
#include "decalc.h"
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//This class was created using the algorythms described in the
// "Evaluating putative chimeric sequences from PCR-amplified products" paper
//by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
class Ccode : public Chimera {
public:
- Ccode(string, string);
+ Ccode(string, string, string);
~Ccode();
- void getChimeras();
+ int getChimeras();
void print(ostream&);
void setCons(string c) {}
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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