X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=e4c2e0b6748eb6c795c8a171e1f1e8a6fb380f6f;hb=d635b39347cd81943ea50de7b813a0a5d743b0c0;hp=a904a10b683ce3fd04784e9ac1a60d02e293c368;hpb=0fb6d165c8dc8dc7153a101513a05f457431d0bc;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index a904a10..e4c2e0b 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -14,38 +14,51 @@
 #include "command.hpp"
 #include "sequence.hpp"
 #include "qualityscores.h"
+#include "groupmap.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:
-
+	
+	GroupMap* groupMap;
+	
 	struct linePair {
 		unsigned long int start;
-		int num;
-		linePair(unsigned long int i, int j) : start(i), num(j) {}
+		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 keepFirstTrim(Sequence&, QualityScores&);
+	bool removeLastTrim(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;
+	string fastaFile, oligoFile, qFileName, groupfile, outputDir;
 	
 	bool flip, allFiles, qtrim;
 	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
-	int qWindowSize, qWindowStep;
+	int qWindowSize, qWindowStep, keepFirst, removeLast;
 	double qRollAverage, qThreshold, qWindowAverage, qAverage;
 	vector<string> revPrimer, outputNames;
 	set<string> filesToRemove;
@@ -53,6 +66,7 @@ private:
 	vector<string> groupVector;
 	map<string, int> primers;
 	map<string, int> combos;
+	map<string, int> groupToIndex;
 	
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
@@ -60,8 +74,7 @@ private:
 	
 	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*>&);
-	
+	int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
 };
 
 #endif