X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=d40cfe3c5604d66009ba22b568b0df71f3688faa;hb=69c7a1b20fbd9a1877a27fcdf18150405de9c087;hp=21a5d41e759c761a3302340319c857544ffc313e;hpb=fe5bbb79f9434df947347881c47b430112f4253e;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 21a5d41..d40cfe3 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -37,11 +37,12 @@ private:
 		unsigned long int end;
 		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
 	};
-
-	void getOligos(vector<string>&, vector<string>&);
+	
+	void getOligos(vector<vector<string> >&, vector<vector<string> >&);
 	int stripBarcode(Sequence&, QualityScores&, int&);
 	int stripForward(Sequence&, QualityScores&, int&);
 	bool stripReverse(Sequence&, QualityScores&);
+	
 	bool keepFirstTrim(Sequence&, QualityScores&);
 	bool removeLastTrim(Sequence&, QualityScores&);
 
@@ -66,15 +67,17 @@ private:
 	map<string, int> primers;
 	map<string, int> combos;
 	map<string, int> groupToIndex;
-	
+	vector<string> primerNameVector;	//needed here?
+	vector<string> barcodeNameVector;	//needed here?
+	map<string, int> groupCounts;  
+
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
 	vector<linePair*> qLines;
 	
-	int driverCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>, linePair*, linePair*);	
-	int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>);
+	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 setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
-	
 };
 
 #endif