added modify names parameter to set.dir

[mothur.git] / normalizesharedcommand.h

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
index fcfc727b23ba0e4aae0fc1d1406c6799fde81689..53bcd6b5e4aac7d0a463fa436fc8ed6346f5f069 100644 (file)
--- a/normalizesharedcommand.h
+++ b/normalizesharedcommand.h
@@ -12,33 +12,44 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sharedrabundvector.h"
 
-class GlobalData;
-
 class NormalizeSharedCommand : public Command {
 
 public:
        NormalizeSharedCommand(string);
-       ~NormalizeSharedCommand();
-       int execute();
-       void help();
+       NormalizeSharedCommand();
+       ~NormalizeSharedCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "normalize.shared";            }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
+       string getDescription()         { return "normalize samples in a shared or relabund file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        InputData* input;
        vector<SharedRAbundVector*> lookup;
+       vector<SharedRAbundFloatVector*> lookupFloat;
        
-       bool abort, allLines, pickedGroups;
+       bool abort, allLines, pickedGroups, makeRelabund;
        set<string> labels; //holds labels to be used
-       string groups, label, outputDir, method;
+       string groups, label, outputDir, method, sharedfile, relabundfile, format, inputfile;
        int norm;
-       vector<string> Groups;
-       
-       int normalize(vector<SharedRAbundVector*>&, ofstream&);
-       int eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup);
+       vector<string> Groups, outputNames;
+               
+       int normalize(vector<SharedRAbundVector*>&);
+       int normalize(vector<SharedRAbundFloatVector*>&);
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
 
 };