X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=f9a251c9323a9388af285ce6933fd5b676fe3838;hb=17aafaea968f87e581297063b16695ad515bea53;hp=800ec3d047fac0221edde0dec47fb130058519ad;hpb=21784ce4eb9b292db6f6191ed504f5e20754c810;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 800ec3d..f9a251c 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -12,30 +12,52 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "sequence.hpp"
 
 class TrimSeqsCommand : public Command {
 public:
-	TrimSeqsCommand();
+	TrimSeqsCommand(string);
 	~TrimSeqsCommand();
 	int execute();
+	void help();
 	
 private:
-	void getOligos();
-	bool stripBarcode(Sequence&, string&);
+
+	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&);
 	bool stripReverse(Sequence&);
 	bool cullLength(Sequence&);
 	bool cullHomoP(Sequence&);
 	bool cullAmbigs(Sequence&);
-	
-	GlobalData* globaldata;
+	bool compareDNASeq(string, string);
+	bool compareDNASeq(string, string, int, int&, int);
 
-	bool oligos, flip;
-	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength;
-	vector<string> forPrimer, revPrimer;
-	map<string, string> barcodes;
+	bool abort;
+	string fastaFile, oligoFile, qFileName, outputDir;
+	
+	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