X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=b5357b38e1e3bf892ef7f0cd9ffcfb7b7de4ec8a;hb=a86aff4f80701bf0d436f02c0095920114e1cba2;hp=9b02be9ef5ec0f5a50d0563ab87a7f7d053bdadc;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 9b02be9..b5357b3 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -22,25 +22,44 @@ 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&, int&);
 	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;
-	vector<string> forPrimer, revPrimer;
+	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+	vector<string> revPrimer, outputNames;
 	map<string, int> barcodes;
 	vector<string> groupVector;
+	map<string, int> primers;
+	map<string, int> combos;
+	
+	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