X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.h;h=2bf7a70fd159a93fcc813c3236aed97a8c18c916;hb=cd7040a22ae19c86a13c2c10ed90a64b77a0c482;hp=d980288ac3585916321edec15114d0c47303e120;hpb=284fd95c611ccc3b1a7875c4dacfca06d1f50ed6;p=mothur.git

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index d980288..2bf7a70 100644
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -20,9 +20,18 @@
 class ChimeraCcodeCommand : public Command {
 public:
 	ChimeraCcodeCommand(string);
-	~ChimeraCcodeCommand();
-	int execute();
-	void help();
+	ChimeraCcodeCommand();
+	~ChimeraCcodeCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "chimera.ccode";		}
+	string getCommandCategory()		{ return "Sequence Processing"; }
+	string getHelpString();	
+	string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
+	string getDescription()		{ return "detect chimeric sequences"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 		
 private:
@@ -47,8 +56,6 @@ private:
 	Chimera* chimera;
 	vector<string> fastaFileNames;
 	vector<string> outputNames;
-	
-	
 };
 
 /***********************************************************/