added diffs and percent parameters to cluster.fragments command

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 1eb2576d2b6867f132be866b4b3e96b1cc7a1c44..e8ca96a6328ee56cf56ff1e9a1869107b359896f 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -16,7 +16,7 @@
 
 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;
+       string refName, queryName, sequence;
        double errorRate;
        int weight, matches, mismatches, total;
        
@@ -35,13 +35,19 @@ struct Compare {
                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();
        
@@ -54,12 +60,16 @@ private:
        void printErrorHeader();
        void printErrorData(Compare);
        
-       string queryFileName, referenceFileName, namesFileName, errorFileName, outputDir;
+       string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
        double threshold;
        int numRefs;
-       ofstream errorFile;
+       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;
 };
 
 #endif