changes while testing

[mothur.git] / clearcutcommand.h

diff --git a/clearcutcommand.h b/clearcutcommand.h
index ea6e279b88ca0f6d59312936b2c1652ff5b1a9b6..817c4a3290804405bd47582d9b3ec5349c182b43 100644 (file)
--- 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: 
@@ -26,20 +25,26 @@ 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();    
+       ~ClearcutCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "clearcut";                    }
+       string getCommandCategory()             { return "Hypothesis Testing";  }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       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;
-       map<string, vector<string> > outputTypes;
+       
 };
 
 /****************************************************************************/