changes while testing

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index cb715ce05bc1edad8f2790cd78b67a356eafd7c3..aac17b6979910ebc733be840eb37ec720ecc1105 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -10,59 +10,68 @@
  *
  */
 
-#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() {}
+       ~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 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 int start;
-               unsigned long int end;
-               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+               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;
@@ -70,7 +79,7 @@ private:
 
        void getReferences();
        map<string,int> getWeights();
-       Compare getErrors(Sequence, Sequence);
+       int getErrors(Sequence, Sequence, Compare&);
        void printErrorHeader(ofstream&);
        void printErrorData(Compare, int, ofstream&, ofstream&);
        void printSubMatrix();
@@ -78,13 +87,13 @@ private:
        void printErrorQuality(map<char, vector<int> >);
        void printQualityFR(vector<vector<int> >, vector<vector<int> >);
        
-       int setLines(string, string, string, vector<unsigned long int>&, vector<unsigned long int>&, vector<unsigned long 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;
+       string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir, countfile;
        double threshold;
-       bool ignoreChimeras, filter;
+       bool ignoreChimeras, save, aligned;
        int numRefs, processors;
        int maxLength, totalBases, totalMatches;
        //ofstream errorSummaryFile, errorSeqFile;