X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraseqscommand.h;h=7e51748b3b7c8b16bf983e44f0771275f7cd532f;hb=3fd6dd6e4f19a458ac2966ee5458787e998a1bde;hp=f19a79d230642894a8bbb7ab9d459f43368fd5dd;hpb=58cc09a375d1e1afceef3b036574ff21394ccc4d;p=mothur.git

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index f19a79d..7e51748 100644
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,29 +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, namefile;
-	bool filter, correction, svg, printAll;
-	int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity;
-	float divR;
-	Chimera* chimera;
-	
-	
+	vector<string> outputNames;
+	map< string, vector<string> > outputTypes;
+
 };
 
 /***********************************************************/