X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=chimeraccodecommand.h;h=36584e091537138c8d1ab853ee99be68cbc5bcec;hb=bbf90b58a19eb047a7f15ec600db62534b74182c;hp=a9ed223b112cdb50876024c893257549e159481f;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index a9ed223..36584e0 100644
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -21,13 +21,16 @@ class ChimeraCcodeCommand : public Command {
 public:
 	ChimeraCcodeCommand(string);
 	ChimeraCcodeCommand();
-	~ChimeraCcodeCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~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"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 		
 private:
@@ -52,9 +55,6 @@ private:
 	Chimera* chimera;
 	vector<string> fastaFileNames;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
-	
-	
 };
 
 /***********************************************************/