X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.h;h=ea6e279b88ca0f6d59312936b2c1652ff5b1a9b6;hb=7c08fa69c0b89e7a08341af2aa724f206f182075;hp=b3ac28e03a293df1acb1f946fcec755294d0ecf5;hpb=b1bcc272003b50a8c06dc9120754da1f5b744598;p=mothur.git

diff --git a/clearcutcommand.h b/clearcutcommand.h
index b3ac28e..ea6e279 100644
--- a/clearcutcommand.h
+++ b/clearcutcommand.h
@@ -11,7 +11,7 @@
  */
 
 #include "command.hpp"
-
+#include "globaldata.hpp"
 
 /* 
   Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining: 
@@ -25,14 +25,21 @@ class ClearcutCommand : public Command {
 
 public:
 	ClearcutCommand(string);
+	ClearcutCommand();
 	~ClearcutCommand() {};
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();	
 	
 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;
+	map<string, vector<string> > outputTypes;
 };
 
 /****************************************************************************/