X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.h;h=8f3773eef5cafc5b4a18c56da51df9bdb9606be6;hb=8e67e9de1b200106bea5a468ac02125954656499;hp=b3ac28e03a293df1acb1f946fcec755294d0ecf5;hpb=b1bcc272003b50a8c06dc9120754da1f5b744598;p=mothur.git

diff --git a/clearcutcommand.h b/clearcutcommand.h
index b3ac28e..8f3773e 100644
--- a/clearcutcommand.h
+++ b/clearcutcommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 
-
 /* 
   Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining: 
   A Fast Distance-Based Phylogenetic Tree Construction Method, 
@@ -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, stdout, kimura, jukes, protein, DNA, stdin;
+	bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
 	bool abort;
+	vector<string> outputNames;
+	
 };
 
 /****************************************************************************/