X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.h;h=8f3773eef5cafc5b4a18c56da51df9bdb9606be6;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=980431b216ec67c67c3a8bd221055b24f1c98624;hpb=cfe70bbc94980a0177af465d3464db754673bd56;p=mothur.git

diff --git a/clearcutcommand.h b/clearcutcommand.h
index 980431b..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;
 	bool abort;
+	vector<string> outputNames;
+	
 };
 
 /****************************************************************************/