X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=40c221a0ec61c051099d081f15dd87bea135a163;hb=1c898913f53fe4c6574102896b967d9347d1b42a;hp=565d5283329124a65aca975d51a9588cb791670d;hpb=bffbd9ad0d837bc9523d95e7b35c34cfd2631046;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 565d528..40c221a 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -12,31 +12,75 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "sequence.hpp"
+#include "qualityscores.h"
+#include "groupmap.h"
 
 class TrimSeqsCommand : public Command {
 public:
+	TrimSeqsCommand(string);
 	TrimSeqsCommand();
-	~TrimSeqsCommand();
-	int execute();
+	~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:
-	void getOligos();
-	bool stripBarcode(Sequence&, string&);
-	bool stripForward(Sequence&);
-	bool stripReverse(Sequence&);
 	
-	GlobalData* globaldata;
+	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<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&);
 
-	int totalBarcodeCount, matchBarcodeCount; // to be removed
-	int totalFPrimerCount, matchFPrimerCount; // to be removed
-	int totalRPrimerCount, matchRPrimerCount; // to be removed
-	
-	bool oligos, flip;
-	int numFPrimers, numRPrimers;
-	vector<string> forPrimer, revPrimer;
-	map<string, string> barcodes;
+	bool cullLength(Sequence&);
+	bool cullHomoP(Sequence&);
+	bool cullAmbigs(Sequence&);
+	bool compareDNASeq(string, string);
+	int countDiffs(string, string);
+
+	bool abort;
+	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, keepFirst, removeLast;
+	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;
+	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, 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