X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ccode.h;fp=ccode.h;h=456b735df524ff3eed9c2688be95f8537c0d0c86;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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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 "chimera.h"
+#include "dist.h"
+#include "decalc.h"
+
+/***********************************************************/
+//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, bool, string, int, int, string);	//fasta, template, filter, mask, window, numWanted, outputDir
+		~Ccode();
+		
+		int getChimeras(Sequence* query);
+		Sequence print(ostream&, ostream&);
+		
+		#ifdef USE_MPI
+		Sequence print(MPI_File&, MPI_File&);
+		#endif
+	private:
+	
+		Dist* 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); 
+		
+		#ifdef USE_MPI
+		int printMapping(string&);
+		MPI_File outMap;
+		#endif
+
+};
+
+/***********************************************************/
+
+#endif
+
+