X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.h;h=8f3773eef5cafc5b4a18c56da51df9bdb9606be6;hb=cc19310422f125d6628980bd1148e1e816792382;hp=d6c0a57d9628a124c3bc900d6865f0ed4e7cc606;hpb=4a2d841cb97fb02351022efe9d7068b1dc212bf9;p=mothur.git

diff --git a/clearcutcommand.h b/clearcutcommand.h
index d6c0a57..8f3773e 100644
--- a/clearcutcommand.h
+++ b/clearcutcommand.h
@@ -11,7 +11,6 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
 
 /* 
   Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining: 
@@ -25,14 +24,26 @@ class ClearcutCommand : public Command {
 
 public:
 	ClearcutCommand(string);
-	~ClearcutCommand() {};
-	int execute();
-	void help();	
+	ClearcutCommand();
+	~ClearcutCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "clearcut";			}
+	string getCommandCategory()		{ return "Hypothesis Testing";	}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	string getCitation() { return "Sheneman L, Evans J, Foster JA (2006). Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22: 2823-4. \nhttp://www.mothur.org/wiki/Clearcut"; }
+	string getDescription()		{ return "create a tree from a fasta or phylip file"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
-	bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA, stdinWanted;
+	bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
 	bool abort;
+	vector<string> outputNames;
+	
 };
 
 /****************************************************************************/