X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=f9a251c9323a9388af285ce6933fd5b676fe3838;hb=17aafaea968f87e581297063b16695ad515bea53;hp=87b813ff9afa8575855c5cca69916de7287f9d9f;hpb=e7729bb337cfefcaba24549092cc89b44002af39;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 87b813f..f9a251c 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -22,7 +22,14 @@ 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&);
@@ -32,15 +39,25 @@ private:
 	bool cullHomoP(Sequence&);
 	bool cullAmbigs(Sequence&);
 	bool compareDNASeq(string, string);
+	bool compareDNASeq(string, string, int, int&, int);
 
 	bool abort;
-	string fastaFile, oligoFile, qFileName;
+	string fastaFile, oligoFile, qFileName, outputDir;
 	
-	bool flip, allFiles;
-	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage;
-	vector<string> forPrimer, revPrimer;
+	bool flip, allFiles, qtrim;
+	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs, currentSeqsTdiffs;
+	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