changes while testing

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index e8ca96a6328ee56cf56ff1e9a1869107b359896f..aac17b6979910ebc733be840eb37ec720ecc1105 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -10,66 +10,106 @@
  *
  */
 
-#include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
+#include "referencedb.h"
+#include "counttable.h"
 
-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 = "";
-       }
-};
 
 class SeqErrorCommand : public Command {
 public:
        SeqErrorCommand(string);
        SeqErrorCommand();
-       ~SeqErrorCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~SeqErrorCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "seq.error";                           }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nhttp://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();
-       Compare getErrors(Sequence, Sequence);
-       void printErrorHeader();
-       void printErrorData(Compare);
+       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> >);
        
-       string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
+       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, countfile;
        double threshold;
-       int numRefs;
-       ofstream errorSummaryFile, errorSeqFile;
+       bool ignoreChimeras, save, aligned;
+       int numRefs, processors;
+       int maxLength, totalBases, totalMatches;
+       //ofstream errorSummaryFile, errorSeqFile;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        vector<Sequence> referenceSeqs;
        vector<vector<int> > substitutionMatrix;
-       int a,t,g,c,gap,n;
+       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