X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraseqscommand.h;h=7e51748b3b7c8b16bf983e44f0771275f7cd532f;hb=095a4c7aed0cf5ef79eaf28f0d79d3aa51c2811e;hp=3e437ec33c5382b57b2364570a4a4caa094c97ea;hpb=e72551c9cc5542e6a354f0f3e415fea261421d72;p=mothur.git

diff --git a/chimeraseqscommand.h b/chimeraseqscommand.h
index 3e437ec..7e51748 100644
--- a/chimeraseqscommand.h
+++ b/chimeraseqscommand.h
@@ -12,41 +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:
+	vector<string> outputNames;
+	map< string, vector<string> > outputTypes;
 
-	struct linePair {
-		int start;
-		int numSeqs;
-		linePair(long int i, int j) : start(i), numSeqs(j) {}
-	};
-	vector<int> processIDS;   //processid
-	vector<linePair*> lines;
-	
-	int driver(linePair*, string, string);
-	void createProcesses(string, string);
-	void appendOutputFiles(string, string); 
-
-	bool abort;
-	string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile, outputDir, search;
-	bool filter, correction, svg, printAll, realign;
-	int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs;
-	float divR;
-	Chimera* chimera;
-	
-	
 };
 
 /***********************************************************/