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

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 2c5ab237a2d39b006dee4eca4e9b9b2c65a57ebe..f1e7c48cd71ee7ff1984e43cb7bb5676a3ee42a5 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -12,7 +12,6 @@
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "readotu.h"
 
 /* The shared() command:
        The shared command can only be executed after a successful read.shared command.  
@@ -21,20 +20,20 @@
        There are no shared command parameters.  The shared command should be in the following format: shared(). */
 
 
-class GlobalData;
-
 class SharedCommand : public Command {
        
 public:
        SharedCommand(string);  
        SharedCommand();
        ~SharedCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "make.shared";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        void printSharedData(vector<SharedRAbundVector*>);
@@ -42,17 +41,15 @@ private:
        int readOrderFile();
        bool isValidGroup(string, vector<string>);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
-       map<string, vector<string> > outputTypes;
        
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        SharedListVector* SharedList;
        InputData* input;
        GroupMap* groupMap;
-       vector<string> groups, outputNames, order;
+       vector<string> Groups, outputNames, order;
+       set<string> labels;
        ofstream out;
-       string filename, fileroot, outputDir;
-       bool firsttime, pickedGroups;
+       string filename, fileroot, outputDir, listfile, groupfile, ordergroupfile;
+       bool firsttime, pickedGroups, abort, allLines;
        map<string, ofstream*> filehandles;
        map<string, ofstream*>::iterator it3;