X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=40c221a0ec61c051099d081f15dd87bea135a163;hb=1c898913f53fe4c6574102896b967d9347d1b42a;hp=93e8c776918ec9fa2d6f661d7c178380a4f47d66;hpb=6e81846c8e5b2614f6b06643a9f558fb0e6669fa;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 93e8c77..40c221a 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -14,26 +14,41 @@
 #include "command.hpp"
 #include "sequence.hpp"
 #include "qualityscores.h"
+#include "groupmap.h"
 
 class TrimSeqsCommand : public Command {
 public:
 	TrimSeqsCommand(string);
-	~TrimSeqsCommand();
-	int execute();
-	void help();
+	TrimSeqsCommand();
+	~TrimSeqsCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "trim.seqs";	}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-
+	
+	GroupMap* groupMap;
+	
 	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>&);
+	
+	void getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<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&);
@@ -41,11 +56,11 @@ private:
 	int countDiffs(string, string);
 
 	bool abort;
-	string fastaFile, oligoFile, qFileName, outputDir;
+	string fastaFile, oligoFile, qFileName, groupfile, nameFile, 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;
@@ -53,15 +68,19 @@ private:
 	vector<string> groupVector;
 	map<string, int> primers;
 	map<string, int> combos;
-	
+	map<string, int> groupToIndex;
+	vector<string> primerNameVector;	//needed here?
+	vector<string> barcodeNameVector;	//needed here?
+	map<string, int> groupCounts;  
+	map<string, string> nameMap;
+
 	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 driverCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);	
+	int createProcessesCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >);
 	int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
-	
 };
 
 #endif