X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.h;h=cc904ec7f246aed91970b41cf52e39b7d32b896b;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=a012d68e614e82c18a59fe79c115e213a614d35b;hpb=fe5bbb79f9434df947347881c47b430112f4253e;p=mothur.git

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index a012d68..cc904ec 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
+#include "referencedb.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;
@@ -43,31 +44,67 @@ 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"; }
+	string getDescription()		{ return "seq.error"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	bool abort;
+	ReferenceDB* rdb;
+	
+	struct linePair {
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long 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);
+	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> >);
 	
-	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
+	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;
 	double threshold;
-	int numRefs;
-	ofstream errorSummaryFile, errorSeqFile;
+	bool ignoreChimeras, save;
+	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