X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.h;h=f03b5ddcf6b5de00eba42210d39c74e46848d73c;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=d7ffef3c74b965967dd6f68d7a6914183ec2253f;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/getsharedotucommand.h b/getsharedotucommand.h
index d7ffef3..f03b5dd 100644
--- a/getsharedotucommand.h
+++ b/getsharedotucommand.h
@@ -14,6 +14,8 @@
 #include "listvector.hpp"
 #include "sequence.hpp"
 #include "groupmap.h"
+#include "sharedrabundvector.h"
+#include "inputdata.h"
 
 //**********************************************************************************************************************
 class GetSharedOTUCommand : public Command {
@@ -28,9 +30,12 @@ class GetSharedOTUCommand : public Command {
 		string getCommandName()			{ return "get.sharedseqs";			}
 		string getCommandCategory()		{ return "OTU-Based Approaches";	}
 		string getRequiredCommand()		{ return "none";					}
-		string getHelpString();	
+		
+	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()); }	
 	
@@ -41,7 +46,7 @@ class GetSharedOTUCommand : public Command {
 		GroupMap* groupMap;
 		
 		set<string> labels;
-		string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir, format;
+		string fastafile, label, groups, listfile, groupfile, sharedfile, output, userGroups, outputDir, format;
 		bool abort, allLines, unique;
 		vector<string> Groups;
 		map<string, string> groupFinder;
@@ -50,6 +55,8 @@ class GetSharedOTUCommand : public Command {
 		vector<string> outputNames;
 		
 		int process(ListVector*);
+        int process(vector<SharedRAbundVector*>&);
+        int runShared();
 		
 };
 //**********************************************************************************************************************