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

[mothur.git] / subsamplecommand.h

diff --git a/subsamplecommand.h b/subsamplecommand.h
index b00defdd9d63e797675d8a7809e32fe1d92d6a63..6716903105f2fc25d018b77d977d6fa57875a148 100644 (file)
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -11,11 +11,11 @@
  */
  
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "sharedrabundvector.h"
 #include "listvector.hpp"
 #include "rabundvector.hpp"
 #include "inputdata.h"
+#include "sequence.hpp"
 
 
 class SubSampleCommand : public Command {
@@ -23,23 +23,22 @@ class SubSampleCommand : public Command {
 public:
        SubSampleCommand(string);
        SubSampleCommand();
-       ~SubSampleCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~SubSampleCommand() {}
        
-private:
-       GlobalData* globaldata;
+       vector<string> setParameters();
+       string getCommandName()                 { return "sub.sample";  }
+       string getCommandCategory()             { return "General";             }
+       string getHelpString(); 
        
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:       
        bool abort, pickedGroups, allLines, persample;
        string listfile, groupfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
        set<string> labels; //holds labels to be used
        string groups, label, outputDir;
        vector<string> Groups, outputNames;
-       map<string, vector<string> > outputTypes;
        int size;
        vector<string> names;
        map<string, vector<string> > nameMap;