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

[mothur.git] / clustersplitcommand.h

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index 9bce0995ee9cc9d7f212df0296335487502a3fd9..28c7d237dccb8ce31542c76f01378b0f8e053d71 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -16,7 +16,6 @@
 #include "listvector.hpp"
 #include "cluster.hpp"
 #include "sparsematrix.hpp"
-#include "globaldata.hpp"
 
 
 class ClusterSplitCommand : public Command {
@@ -24,20 +23,20 @@ class ClusterSplitCommand : public Command {
 public:
        ClusterSplitCommand(string);
        ClusterSplitCommand();
-       ~ClusterSplitCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~ClusterSplitCommand() {}
        
+       vector<string> setParameters();
+       string getCommandName()                 { return "cluster.split";                       }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+
 private:
-       GlobalData* globaldata;
        vector<int> processIDS;   //processid
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
-
+       
        string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
        double cutoff, splitcutoff;
        int precision, length, processors, taxLevelCutoff;