X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraseqscommand.h;h=7e51748b3b7c8b16bf983e44f0771275f7cd532f;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=85d573246a56f83c73140ac393c96cdf66397097;hpb=7597c66c08bac938fedcacc1f760186bc077b3f1;p=mothur.git

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 85d5732..7e51748 100644
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,28 +12,26 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "chimera.h"
-
 
 /***********************************************************/
 
 class ChimeraSeqsCommand : public Command {
 public:
 	ChimeraSeqsCommand(string);
+	ChimeraSeqsCommand() {}
 	~ChimeraSeqsCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map< string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 	
 		
 private:
-	
-	bool abort;
-	string method, fastafile, templatefile, consfile, quanfile, maskfile;
-	bool filter, correction;
-	int processors, midpoint, averageLeft, averageRight, window, iters, increment;
-	Chimera* chimera;
-	
-	
+	vector<string> outputNames;
+	map< string, vector<string> > outputTypes;
+
 };
 
 /***********************************************************/