added amova command

[mothur.git] / normalizesharedcommand.h

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
index fcfc727b23ba0e4aae0fc1d1406c6799fde81689..bedff43da2532c99d2e672c27f0abc5a8ebbc9b8 100644 (file)
--- a/normalizesharedcommand.h
+++ b/normalizesharedcommand.h
@@ -12,7 +12,6 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sharedrabundvector.h"
 
 class GlobalData;
@@ -21,24 +20,32 @@ class NormalizeSharedCommand : public Command {
 
 public:
        NormalizeSharedCommand(string);
+       NormalizeSharedCommand();
        ~NormalizeSharedCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
 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;
        int norm;
-       vector<string> Groups;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
        
        int normalize(vector<SharedRAbundVector*>&, ofstream&);
-       int eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup);
+       int normalize(vector<SharedRAbundFloatVector*>&, ofstream&);
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
 
 };