X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=40c221a0ec61c051099d081f15dd87bea135a163;hb=1c898913f53fe4c6574102896b967d9347d1b42a;hp=c5cbd3da1b0044467e8558a5619dc651434bcffe;hpb=df905918ace8537273616b4120d404ebd29dc9cc;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index c5cbd3d..40c221a 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -20,13 +20,16 @@ class TrimSeqsCommand : public Command {
 public:
 	TrimSeqsCommand(string);
 	TrimSeqsCommand();
-	~TrimSeqsCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~TrimSeqsCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "trim.seqs";	}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	
@@ -38,7 +41,7 @@ private:
 		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
 	};
 	
-	void getOligos(vector<vector<string> >&, vector<vector<string> >&);
+	void getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
 	int stripBarcode(Sequence&, QualityScores&, int&);
 	int stripForward(Sequence&, QualityScores&, int&);
 	bool stripReverse(Sequence&, QualityScores&);
@@ -51,10 +54,9 @@ private:
 	bool cullAmbigs(Sequence&);
 	bool compareDNASeq(string, string);
 	int countDiffs(string, string);
-	map<string, vector<string> > outputTypes;
 
 	bool abort;
-	string fastaFile, oligoFile, qFileName, groupfile, outputDir;
+	string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
 	
 	bool flip, allFiles, qtrim;
 	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
@@ -69,14 +71,15 @@ private:
 	map<string, int> groupToIndex;
 	vector<string> primerNameVector;	//needed here?
 	vector<string> barcodeNameVector;	//needed here?
-	vector<int> groupCounts;  //same order as barcodeNameVector
+	map<string, int> groupCounts;  
+	map<string, string> nameMap;
 
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
 	vector<linePair*> qLines;
 	
-	int driverCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);	
-	int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
+	int driverCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);	
+	int createProcessesCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >);
 	int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
 };