a few meaningless changes that are commented out

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index c8dd4efb232b4e5c2ce0727c8d5badaf2433d6a9..19fcd4731d22edc39383003b62c796242b7a4363 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -43,13 +43,15 @@ 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(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        bool abort;
@@ -58,16 +60,22 @@ private:
        map<string,int> getWeights();
        Compare getErrors(Sequence, Sequence);
        void printErrorHeader();
-       void printErrorData(Compare);
-       
-       string queryFileName, referenceFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
+       void printErrorData(Compare, int);
+       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, outputDir;
        double threshold;
+       bool ignoreChimeras;
        int numRefs;
+       int maxLength;
        ofstream errorSummaryFile, errorSeqFile;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        vector<Sequence> referenceSeqs;
+       vector<vector<int> > substitutionMatrix;
 };
 
 #endif