changes while testing

[mothur.git] / getsharedotucommand.h

diff --git a/getsharedotucommand.h b/getsharedotucommand.h
index 5b5516c3a3d6850aa36cce33b104c888872b9137..f03b5ddcf6b5de00eba42210d39c74e46848d73c 100644 (file)
--- a/getsharedotucommand.h
+++ b/getsharedotucommand.h
@@ -14,7 +14,8 @@
 #include "listvector.hpp"
 #include "sequence.hpp"
 #include "groupmap.h"
-#include "globaldata.hpp"
+#include "sharedrabundvector.h"
+#include "inputdata.h"
 
 //**********************************************************************************************************************
 class GetSharedOTUCommand : public Command {
@@ -22,25 +23,40 @@ class GetSharedOTUCommand : public Command {
        public:
        
                GetSharedOTUCommand(string);    
-               ~GetSharedOTUCommand();
-               int execute();
-               void help();    
+               GetSharedOTUCommand();  
+               ~GetSharedOTUCommand() {}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.sharedseqs";                      }
+               string getCommandCategory()             { return "OTU-Based Approaches";        }
+               string getRequiredCommand()             { return "none";                                        }
                
-       private:
+       string getHelpString(); 
+    string getOutputPattern(string);   
+               string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
+               string getDescription()         { return "identifies sequences that are either unique or shared by specific groups"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
                
-               GlobalData* globaldata;
+       private:
                ListVector* list;
                GroupMap* groupMap;
                
                set<string> labels;
-               string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir;
+               string fastafile, label, groups, listfile, groupfile, sharedfile, 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;
                
-               void process(ListVector*);
+               int process(ListVector*);
+        int process(vector<SharedRAbundVector*>&);
+        int runShared();
                
 };
 //**********************************************************************************************************************