X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=a4a4215277fadbdb5857dea6d9e9319e233cad01;hb=e21aedb9ffeabff18207d53e9cc5420d2e30a5b2;hp=a93eba072eef5f9b6dd62b578331ee862272e76b;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index a93eba0..a4a4215 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -22,25 +22,42 @@ public:
 	void help();
 	
 private:
-	void getOligos(vector<ofstream*>&);
+
+	struct linePair {
+		int start;
+		int num;
+		linePair(long int i, int j) : start(i), num(j) {}
+	};
+
+	void getOligos(vector<string>&);
 	bool stripQualThreshold(Sequence&, ifstream&);
 	bool cullQualAverage(Sequence&, ifstream&);
-	bool stripBarcode(Sequence&, int&);
-	bool stripForward(Sequence&);
+	int stripBarcode(Sequence&, int&);
+	int stripForward(Sequence&);
 	bool stripReverse(Sequence&);
 	bool cullLength(Sequence&);
 	bool cullHomoP(Sequence&);
 	bool cullAmbigs(Sequence&);
 	bool compareDNASeq(string, string);
+	int countDiffs(string, string);//, int, int&, int);
 
 	bool abort;
 	string fastaFile, oligoFile, qFileName, outputDir;
 	
 	bool flip, allFiles, qtrim;
-	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage;
+	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs;
 	vector<string> forPrimer, revPrimer, outputNames;
 	map<string, int> barcodes;
 	vector<string> groupVector;
+	
+	vector<int> processIDS;   //processid
+	vector<linePair*> lines;
+	vector<linePair*> qLines;
+	
+	int driverCreateTrim(string, string, string, string, string, vector<string>, linePair*, linePair*);	
+	int createProcessesCreateTrim(string, string, string, string, string, vector<string>);
+	int setLines(string, vector<linePair*>&);
+	
 };
 
 #endif