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

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
deleted file mode 100644 (file)
index e7c97e1..0000000
--- a/seqerrorcommand.h
+++ /dev/null
@@ -1,112 +0,0 @@
-#ifndef SEQERRORCOMMAND
-#define SEQERRORCOMMAND
-
-/*
- *  seqerrorcommand.h
- *  Mothur
- *
- *  Created by Pat Schloss on 7/15/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "sequence.hpp"
-#include "referencedb.h"
-
-
-class SeqErrorCommand : public Command {
-public:
-       SeqErrorCommand(string);
-       SeqErrorCommand();
-       ~SeqErrorCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "seq.error";                           }
-       string getCommandCategory()             { return "Sequence Processing";         }
-       string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
-       string getDescription()         { return "seq.error"; }
-
-       
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-private:
-       bool abort;
-       ReferenceDB* rdb;
-       
-       struct linePair {
-               unsigned long long start;
-               unsigned long long end;
-               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
-        ~linePair(){}
-       };
-       
-    struct Compare {
-        int AA, AT, AG, AC,    TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, CC, NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
-        string refName, queryName, sequence;
-        double errorRate;
-        int weight, matches, mismatches, total;
-        
-        Compare(){
-            AA=0; AT=0; AG=0; AC=0;
-            TA=0; TT=0; TG=0; TC=0;
-            GA=0; GT=0; GG=0; GC=0;
-            CA=0; CT=0; CG=0; CC=0;
-            NA=0; NT=0; NG=0; NC=0;
-            Ai=0; Ti=0; Gi=0; Ci=0; Ni=0;
-            dA=0; dT=0; dG=0; dC=0;
-            refName = "";
-            queryName = "";
-            weight = 1;
-            matches = 0;
-            mismatches = 0;
-            total = 0;
-            errorRate = 1.0000;
-            sequence = "";
-        }
-        ~Compare(){};
-    };
-
-       vector<int> processIDS;   //processid
-       vector<linePair> lines;
-       vector<linePair> qLines;
-       vector<linePair> rLines;
-
-       void getReferences();
-       map<string,int> getWeights();
-       int getErrors(Sequence, Sequence, Compare&);
-       void printErrorHeader(ofstream&);
-       void printErrorData(Compare, int, ofstream&, ofstream&);
-       void printSubMatrix();
-       void printErrorFRFile(map<char, vector<int> >, map<char, vector<int> >);
-       void printErrorQuality(map<char, vector<int> >);
-       void printQualityFR(vector<vector<int> >, vector<vector<int> >);
-       
-       int setLines(string, string, string, vector<unsigned long long>&, vector<unsigned long long>&, vector<unsigned long long>&);
-       int driver(string, string, string, string, string, string, linePair, linePair, linePair);
-       int createProcesses(string, string, string, string, string, string);
-
-       string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
-       double threshold;
-       bool ignoreChimeras, save;
-       int numRefs, processors;
-       int maxLength, totalBases, totalMatches;
-       //ofstream errorSummaryFile, errorSeqFile;
-       vector<string> outputNames;
-       
-       vector<Sequence> referenceSeqs;
-       vector<vector<int> > substitutionMatrix;
-       vector<vector<int> > qualForwardMap;
-       vector<vector<int> > qualReverseMap;
-       vector<int> misMatchCounts;
-       map<char, vector<int> > qScoreErrorMap;
-       map<char, vector<int> > errorForward;
-       map<char, vector<int> > errorReverse;
-       map<string, int> weights;
-       vector<string> megaAlignVector;
-
-};
-
-#endif