X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=ee79d777a8d11ffaa2e279e69463314f9c3b8938;hb=cd37904452dc95b183ff313ff05720c562902487;hp=565d5283329124a65aca975d51a9588cb791670d;hpb=bffbd9ad0d837bc9523d95e7b35c34cfd2631046;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 565d528..ee79d77 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -12,31 +12,35 @@
 
 #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&);
+	void getOligos(vector<ofstream*>&, vector<ofstream*>&);
+	bool stripQualThreshold(Sequence&, ifstream&);
+	bool cullQualAverage(Sequence&, ifstream&);
+	bool stripBarcode(Sequence&, int&);
 	bool stripForward(Sequence&);
 	bool stripReverse(Sequence&);
-	
-	GlobalData* globaldata;
+	bool cullLength(Sequence&);
+	bool cullHomoP(Sequence&);
+	bool cullAmbigs(Sequence&);
+	bool compareDNASeq(string, string);
 
-	int totalBarcodeCount, matchBarcodeCount; // to be removed
-	int totalFPrimerCount, matchFPrimerCount; // to be removed
-	int totalRPrimerCount, matchRPrimerCount; // to be removed
+	bool abort;
+	string fastaFile, oligoFile, qFileName;
 	
-	bool oligos, flip;
-	int numFPrimers, numRPrimers;
+	bool flip, allFiles;
+	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage;
 	vector<string> forPrimer, revPrimer;
-	map<string, string> barcodes;
+	map<string, int> barcodes;
+	vector<string> groupVector;
 };
 
 #endif