X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.h;h=cb715ce05bc1edad8f2790cd78b67a356eafd7c3;hb=f06fdb807822f8e06db003ed809c87250905cfc8;hp=1194d42f2dfca3a8eedf3d379a7bd3aa3bd50661;hpb=9f4c08cab5a7a9a0e156bd4a5a3a478b476162dc;p=mothur.git

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 1194d42..cb715ce 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -43,38 +43,64 @@ 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 getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	bool abort;
+	
+	struct linePair {
+		unsigned long int start;
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+	};
+	
+	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);
+	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> >);
+	
+	int setLines(string, string, string, vector<unsigned long int>&, vector<unsigned long int>&, vector<unsigned long int>&);
+	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;
 	double threshold;
-	bool ignoreChimeras;
-	int numRefs;
-	int maxLength;
-	ofstream errorSummaryFile, errorSeqFile;
+	bool ignoreChimeras, filter;
+	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;
+	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