X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.h;h=f03b5ddcf6b5de00eba42210d39c74e46848d73c;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=0e25721b6ca2bcd53967261e7fab18bb0dbead54;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/getsharedotucommand.h b/getsharedotucommand.h
index 0e25721..f03b5dd 100644
--- 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 {
@@ -23,31 +24,39 @@ 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";					}
 		
-	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;
-		map<string, vector<string> > outputTypes;
 		
 		int process(ListVector*);
+        int process(vector<SharedRAbundVector*>&);
+        int runShared();
 		
 };
 //**********************************************************************************************************************