X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=c5a94839cd82427c193e3e78a71c8e8434636653;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=e2b0687e2108bc2f6bc95201917dd08d67f757bf;hpb=64ec96a433d3ad3a61a75c6fc08df8d8b6ff36ac;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index e2b0687..c5a9483 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -13,51 +13,73 @@
 #include "mothur.h"
 #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 {
-		int start;
-		int num;
-		linePair(long int i, int j) : start(i), num(j) {}
+		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> >&);
+	int stripBarcode(Sequence&, QualityScores&, int&);
+	int stripForward(Sequence&, QualityScores&, int&);
+	bool stripReverse(Sequence&, QualityScores&);
+	
+	bool keepFirstTrim(Sequence&, QualityScores&);
+	bool removeLastTrim(Sequence&, QualityScores&);
 
-	void getOligos(vector<string>&);
-	bool stripQualThreshold(Sequence&, ifstream&);
-	bool cullQualAverage(Sequence&, ifstream&);
-	bool stripBarcode(Sequence&, int&);
-	bool stripForward(Sequence&);
-	bool stripReverse(Sequence&);
 	bool cullLength(Sequence&);
 	bool cullHomoP(Sequence&);
 	bool cullAmbigs(Sequence&);
 	bool compareDNASeq(string, string);
-	int countDiffs(string, string);//, int, int&, int);
+	int countDiffs(string, string);
 
 	bool abort;
-	string fastaFile, oligoFile, qFileName, outputDir;
+	string fastaFile, oligoFile, qFileName, groupfile, outputDir;
 	
 	bool flip, allFiles, qtrim;
-	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs;
-	vector<string> forPrimer, revPrimer, outputNames;
+	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;  
+
 	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 setLines(string, vector<linePair*>&);
-	
+	int driverCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);	
+	int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
+	int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
 };
 
 #endif