X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=d43eaa484aad5be4403d7967a6abda1e066a127c;hb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;hp=e4c2e0b6748eb6c795c8a171e1f1e8a6fb380f6f;hpb=d635b39347cd81943ea50de7b813a0a5d743b0c0;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index e4c2e0b..d43eaa4 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -38,7 +38,7 @@ private:
 		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&);
@@ -67,13 +67,15 @@ private:
 	map<string, int> primers;
 	map<string, int> combos;
 	map<string, int> groupToIndex;
-	
+	vector<string> primerNameVector;	//needed here?
+	vector<string> barcodeNameVector;	//needed here?
+
 	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>&);
 };