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#ifndef CCODE_H
#define CCODE_H
/*
* ccode.h
* Mothur
*
* Created by westcott on 8/24/09.
* Copyright 2009 Schloss LAB. All rights reserved.
*
*/
#include "mothurchimera.h"
#include "calculator.h"
#include "decalc.h"
/***********************************************************/
//This class was created using the algorithms 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 MothurChimera {
public:
Ccode(string, string, bool, string, int, int, string); //fasta, template, filter, mask, window, numWanted, outputDir
~Ccode();
int getChimeras(Sequence* query);
Sequence print(ostream&, ostream&);
private:
DistCalc* distCalc;
DeCalculator* decalc;
int iters, window, numWanted;
string fastafile, mapInfo;
Sequence* querySeq;
map<int, int> spotMap;
map<int, int>::iterator it;
vector<int> windows; //windows is the vector of window breaks for query
int windowSizes; //windowSizes is the size of the windows for query
map<int, int> trim; //trim is the map containing the starting and ending positions for query
vector<SeqDist> closest; //closest is a vector of sequence at are closest to query
vector<float> averageRef; //averageRef is the average distance at each window for the references for query
vector<float> averageQuery; //averageQuery is the average distance at each winow for the query for query
vector<float> sumRef; //sumRef is the sum of distances at each window for the references for query
vector<float> sumSquaredRef; //sumSquaredRef is the sum of squared distances at each window for the references for query
vector<float> sumQuery; //sumQuery is the sum of distances at each window for the comparison of query to references for query
vector<float> sumSquaredQuery; //sumSquaredQuery is the sum of squared distances at each window for the comparison of query to references for query
vector<float> varRef; //varRef is the variance among references seqs at each window for query
vector<float> varQuery; //varQuery is the variance among references and query at each window
vector<float> sdRef; //sdRef is the standard deviation of references seqs at each window for query
vector<float> sdQuery; //sdQuery is the standard deviation of references and query at each window
vector<float> anova; //anova is the vector of anova scores for each window for query
int refCombo; //refCombo is the number of reference sequences combinations for query
vector<bool> isChimericConfidence; //isChimericConfidence indicates whether query is chimeric at a given window according to the confidence limits
vector<bool> isChimericTStudent; //isChimericConfidence indicates whether query is chimeric at a given window according to the confidence limits
vector<bool> isChimericANOVA; //isChimericConfidence indicates whether query is chimeric at a given window according to the confidence limits
vector<SeqDist> findClosest(Sequence*, int);
void removeBadReferenceSeqs(vector<SeqDist>&); //removes sequences from closest that are to different of too similar to eachother.
void trimSequences(Sequence*);
vector<int> findWindows();
void getAverageRef(vector<SeqDist>); //fills sumRef, averageRef, sumSquaredRef and refCombo.
void getAverageQuery (vector<SeqDist>, Sequence*); //fills sumQuery, averageQuery, sumSquaredQuery.
void findVarianceRef (); //fills varRef and sdRef also sets minimum error rate to 0.001 to avoid divide by 0.
void findVarianceQuery (); //fills varQuery and sdQuery
void determineChimeras (); //fills anova, isChimericConfidence, isChimericTStudent and isChimericANOVA.
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);
};
/***********************************************************/
#endif
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