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

[mothur.git] / getsharedotucommand.h

diff --git a/getsharedotucommand.h b/getsharedotucommand.h
index 0e25721b6ca2bcd53967261e7fab18bb0dbead54..27a57b0242a92c95f694a941b4e2c05ed465c384 100644 (file)
--- a/getsharedotucommand.h
+++ b/getsharedotucommand.h
@@ -14,7 +14,6 @@
 #include "listvector.hpp"
 #include "sequence.hpp"
 #include "groupmap.h"
-#include "globaldata.hpp"
 
 //**********************************************************************************************************************
 class GetSharedOTUCommand : public Command {
@@ -23,29 +22,31 @@ class GetSharedOTUCommand : public Command {
        
                GetSharedOTUCommand(string);    
                GetSharedOTUCommand();  
-               ~GetSharedOTUCommand();
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
+               ~GetSharedOTUCommand() {}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.sharedseqs";                      }
+               string getCommandCategory()             { return "OTU-Based Approaches";        }
+               string getRequiredCommand()             { return "none";                                        }
+               string getHelpString(); 
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
                
        private:
-               
-               GlobalData* globaldata;
                ListVector* list;
                GroupMap* groupMap;
                
                set<string> labels;
-               string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir;
+               string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir, format;
                bool abort, allLines, unique;
                vector<string> Groups;
                map<string, string> groupFinder;
                map<string, string>::iterator it;
                vector<Sequence> seqs;
                vector<string> outputNames;
-               map<string, vector<string> > outputTypes;
                
                int process(ListVector*);