added design parameter to the indicator command

[mothur.git] / readtreecommand.h

diff --git a/readtreecommand.h b/readtreecommand.h
index e9424b2be6d534c61dca64195e2272d7782e0aa4..97391d0982bbadb437ebe13318c47babeca4a981 100644 (file)
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -10,8 +10,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
 #include "readtree.h"
 #include "treemap.h"
@@ -20,15 +18,29 @@ class GlobalData;
 
 class ReadTreeCommand : public Command {
 public:
-       ReadTreeCommand();
+       ReadTreeCommand(string);
+       ReadTreeCommand() {}
        ~ReadTreeCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
        ReadTree* read;
        TreeMap* treeMap;
-       string filename;
+       string filename, treefile, groupfile, namefile;
+       bool abort;
+       map<string, string> nameMap;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       
+       int readNamesFile();
+       int numUniquesInName;
+
 };