X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=137cb735719fba42f0d103af842de80c9930cc3e;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=2d0eabc1aa5a1504d23d1fc146f525504f3213f9;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 2d0eabc..137cb73 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -26,7 +26,9 @@ public:
 	string getCommandName()			{ return "trim.seqs";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
 	string getHelpString();	
-	
+	string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
+	string getDescription()		{ return "provides the preprocessing features needed to screen and sort pyrosequences"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
@@ -35,27 +37,20 @@ 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) {}
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long 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 getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
 	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);
 
-	bool abort;
-	string fastaFile, oligoFile, qFileName, groupfile, outputDir;
+	bool abort, createGroup;
+	string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
 	
 	bool flip, allFiles, qtrim;
 	int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
@@ -71,14 +66,15 @@ private:
 	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<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>&);
+	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 long>&, vector<unsigned long long>&);
 };
 
 #endif