removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / clearcutcommand.h

diff --git a/clearcutcommand.h b/clearcutcommand.h
index ea6e279b88ca0f6d59312936b2c1652ff5b1a9b6..af456566b241a5592b710c01d7d0486090c80705 100644 (file)
--- a/clearcutcommand.h
+++ b/clearcutcommand.h
@@ -26,20 +26,22 @@ 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(); 
+       
+       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;
+       
 };
 
 /****************************************************************************/