some changes to trim.flows

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index e4c2e0b6748eb6c795c8a171e1f1e8a6fb380f6f..c5cbd3da1b0044467e8558a5619dc651434bcffe 100644 (file)
--- 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 +67,16 @@ 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> groupCounts;  //same order as barcodeNameVector
+
        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>&);
 };