X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getsharedotucommand.h;h=f03b5ddcf6b5de00eba42210d39c74e46848d73c;hp=27a57b0242a92c95f694a941b4e2c05ed465c384;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/getsharedotucommand.h b/getsharedotucommand.h
index 27a57b0..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 {
@@ -28,8 +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()); }	
 	
@@ -40,7 +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;
@@ -49,6 +55,8 @@ class GetSharedOTUCommand : public Command {
 		vector<string> outputNames;
 		
 		int process(ListVector*);
+        int process(vector<SharedRAbundVector*>&);
+        int runShared();
 		
 };
 //**********************************************************************************************************************