X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.h;h=2d0eabc1aa5a1504d23d1fc146f525504f3213f9;hb=643cdf74ccd4fc2d565168716fb5645917dee834;hp=d43eaa484aad5be4403d7967a6abda1e066a127c;hpb=03acfa01ede71b107817966fcf27cd728038b3c9;p=mothur.git

diff --git a/trimseqscommand.h b/trimseqscommand.h
index d43eaa4..2d0eabc 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -20,13 +20,15 @@ class TrimSeqsCommand : public Command {
 public:
 	TrimSeqsCommand(string);
 	TrimSeqsCommand();
-	~TrimSeqsCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~TrimSeqsCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "trim.seqs";	}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	
@@ -51,7 +53,6 @@ private:
 	bool cullAmbigs(Sequence&);
 	bool compareDNASeq(string, string);
 	int countDiffs(string, string);
-	map<string, vector<string> > outputTypes;
 
 	bool abort;
 	string fastaFile, oligoFile, qFileName, groupfile, outputDir;
@@ -69,6 +70,7 @@ private:
 	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;