moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / ccode.h

diff --git a/ccode.h b/ccode.h
deleted file mode 100644 (file)
index 456b735..0000000
--- a/ccode.h
+++ /dev/null
@@ -1,93 +0,0 @@
-#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
-
-