X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=a904a10b683ce3fd04784e9ac1a60d02e293c368;hb=0fb6d165c8dc8dc7153a101513a05f457431d0bc;hp=f9a251c9323a9388af285ce6933fd5b676fe3838;hpb=17aafaea968f87e581297063b16695ad515bea53;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index f9a251c..a904a10 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
+#include "qualityscores.h"
 
 class TrimSeqsCommand : public Command {
 public:
@@ -24,38 +25,41 @@ public:
 private:
 
 	struct linePair {
-		int start;
+		unsigned long int start;
 		int num;
-		linePair(long int i, int j) : start(i), num(j) {}
+		linePair(unsigned 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&);
+	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);
-	bool compareDNASeq(string, string, int, int&, int);
+	int countDiffs(string, string);
 
 	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;
+	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, vector<string>, linePair*, linePair*);	
-	int createProcessesCreateTrim(string, string, string, string, string, vector<string>);
+	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, vector<linePair*>&);
 	
 };