X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=137cb735719fba42f0d103af842de80c9930cc3e;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=40c221a0ec61c051099d081f15dd87bea135a163;hpb=1c898913f53fe4c6574102896b967d9347d1b42a;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 40c221a..137cb73 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -27,7 +27,8 @@ public:
 	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()); }	
 	
@@ -36,26 +37,19 @@ 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> >&, 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;
+	bool abort, createGroup;
 	string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
 	
 	bool flip, allFiles, qtrim;
@@ -80,7 +74,7 @@ private:
 	
 	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>&);
+	int setLines(string, string, vector<unsigned long long>&, vector<unsigned long long>&);
 };
 
 #endif