added pipeline commands which involved change to command factory and command class...

[mothur.git] / chimeraseqscommand.h

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 85d573246a56f83c73140ac393c96cdf66397097..7e51748b3b7c8b16bf983e44f0771275f7cd532f 100644 (file)
--- 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;
+
 };
 
 /***********************************************************/