added modify names parameter to set.dir

[mothur.git] / clusterdoturcommand.h

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index da2f4a7c000bb8b2ed0737c2b57dcc5d2569ccae..ccfe03bb74c42d43921f8a8224c210bc7a3a7ab0 100644 (file)
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -12,7 +12,6 @@
 
 #include "command.hpp"
 #include "nameassignment.hpp"
-#include "globaldata.hpp"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
@@ -23,17 +22,23 @@ class ClusterDoturCommand : public Command {
 public:
        ClusterDoturCommand(string);
        ClusterDoturCommand();
-       ~ClusterDoturCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~ClusterDoturCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "cluster.classic";             }
+       string getCommandCategory()             { return "Clustering";                  }
+    
+       string getHelpString(); 
+    string getOutputPattern(string);           
+       string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster.classic\n";}
+       string getDescription()         { return "cluster your sequences into OTUs using DOTUR’s method"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       bool abort, hard;
-       string method, fileroot, tag, outputDir, phylipfile, namefile;
+       bool abort, hard, sim;
+       string method, fileroot, tag, outputDir, phylipfile, namefile, countfile;
        double cutoff;
        int precision, length;
        ofstream sabundFile, rabundFile, listFile;
@@ -45,7 +50,6 @@ private:
        
        void printData(string label);
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
 };
 
 #endif