X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=93e8c776918ec9fa2d6f661d7c178380a4f47d66;hb=b20d7d9b1b0eeeaedb78d8fdf26833fd212d2e81;hp=0a34ff303e618839e3fd80583e91f9ab10305ff8;hpb=64eee3a595ae53817f52807d7393b22e74e31f56;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 0a34ff3..93e8c77 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -12,33 +12,56 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
+#include "sequence.hpp"
+#include "qualityscores.h"
 
 class TrimSeqsCommand : public Command {
 public:
-	TrimSeqsCommand();
+	TrimSeqsCommand(string);
 	~TrimSeqsCommand();
 	int execute();
+	void help();
 	
 private:
-	void getOligos();
-	bool stripBarcode(Sequence&, string&);
-	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);
+
+	bool abort;
+	string fastaFile, oligoFile, qFileName, outputDir;
 	
-	GlobalData* globaldata;
+	bool flip, allFiles, qtrim;
+	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;
 	
-	int totalBarcodeCount, matchBarcodeCount;
-	int totalFPrimerCount, matchFPrimerCount;
-	int totalRPrimerCount, matchRPrimerCount;
+	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>&);
 	
-	bool oligos, flip;
-	int forwardPrimerMismatch, reversePrimerMismatch, barcodeMismatch;
-	int numFPrimers, numRPrimers;
-	vector<string> forPrimer, revPrimer;
-	map<string, string> barcodes;
-
 };
 
 #endif