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

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 7a17c9de22a4c08b8d44a6e59ea3c6f07f18430a..d8f8f0905ba3c3e8c09dfb8ec83ec34f817db89e 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -12,10 +12,8 @@
  /* The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin. */
 
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "fastamap.h"
 #include "groupmap.h"
 #include "readmatrix.hpp"
@@ -40,18 +38,19 @@ class GetOTURepCommand : public Command {
 public:
        GetOTURepCommand(string);
        GetOTURepCommand();
-       ~GetOTURepCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
-
+       ~GetOTURepCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.oturep";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
 private:
-       GlobalData* globaldata;
        ListVector* list;
-       ReadOTUFile* read;
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
@@ -72,7 +71,6 @@ private:
        vector<SeqMap> seqVec;                  // contains maps with sequence index and distance
                                                                        // for all distances related to a certain sequence
        vector<int> rowPositions;
-       map<string, vector<string> > outputTypes;
 
        void readNamesFile();
        void readNamesFile(bool);
@@ -80,8 +78,6 @@ private:
        SeqMap getMap(int);
        string findRep(vector<string>);         // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
        int processNames(string, string);
-                                                                                               
-
 };
 
 #endif