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

[mothur.git] / normalizesharedcommand.h

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
index bedff43da2532c99d2e672c27f0abc5a8ebbc9b8..26bc0e4ca542de7a7c56cf2299918ce0f2819e70 100644 (file)
--- a/normalizesharedcommand.h
+++ b/normalizesharedcommand.h
@@ -14,34 +14,33 @@
 #include "inputdata.h"
 #include "sharedrabundvector.h"
 
-class GlobalData;
-
 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();
+       ~NormalizeSharedCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "normalize.shared";            }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
        InputData* input;
        vector<SharedRAbundVector*> lookup;
        vector<SharedRAbundFloatVector*> lookupFloat;
        
        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, outputNames;
-       map<string, vector<string> > outputTypes;
-       
+               
        int normalize(vector<SharedRAbundVector*>&, ofstream&);
        int normalize(vector<SharedRAbundFloatVector*>&, ofstream&);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);