X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=20b11a85ac05e57b453906475d73ab4fd2ecb2e0;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=9b02be9ef5ec0f5a50d0563ab87a7f7d053bdadc;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 9b02be9..20b11a8 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -13,34 +13,61 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
+#include "qualityscores.h"
 
 class TrimSeqsCommand : public Command {
 public:
 	TrimSeqsCommand(string);
+	TrimSeqsCommand();
 	~TrimSeqsCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 	
 private:
-	void getOligos(vector<ofstream*>&);
-	bool stripQualThreshold(Sequence&, ifstream&);
-	bool cullQualAverage(Sequence&, ifstream&);
-	bool stripBarcode(Sequence&, int&);
-	bool stripForward(Sequence&);
-	bool stripReverse(Sequence&);
+
+	struct linePair {
+		unsigned long int start;
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+	};
+
+	void getOligos(vector<string>&, vector<string>&);
+	int stripBarcode(Sequence&, QualityScores&, int&);
+	int stripForward(Sequence&, QualityScores&, int&);
+	bool stripReverse(Sequence&, QualityScores&);
 	bool cullLength(Sequence&);
 	bool cullHomoP(Sequence&);
 	bool cullAmbigs(Sequence&);
 	bool compareDNASeq(string, string);
+	int countDiffs(string, string);
+	map<string, vector<string> > outputTypes;
 
 	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, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+	int qWindowSize, qWindowStep;
+	double qRollAverage, qThreshold, qWindowAverage, qAverage;
+	vector<string> revPrimer, outputNames;
+	set<string> filesToRemove;
 	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, string, string, vector<string>, vector<string>, linePair*, linePair*);	
+	int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>);
+	int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
+	
 };
 
 #endif