X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.h;h=19fcd4731d22edc39383003b62c796242b7a4363;hb=92de7f976371d41441ad41f02ca83af8b43cef5c;hp=c8dd4efb232b4e5c2ce0727c8d5badaf2433d6a9;hpb=85af0d7ce5839dfd39981811f149157c305dd31a;p=mothur.git

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index c8dd4ef..19fcd47 100644
--- 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