X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=3467c7b1d9e6beb1bcd2b5af9a63f9d9bbaf8045;hb=29c0d3ec01be5372807eb86261100d77de253787;hp=20e2ddb3981df57f471970da64e3631814a6c170;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index 20e2ddb..3467c7b 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -12,8 +12,7 @@
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "shared.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 
 /* The shared() command:
 	The shared command can only be executed after a successful read.shared command.  
@@ -30,17 +29,20 @@ public:
 	SharedCommand();	
 	~SharedCommand();
 	int execute();	
+	void help() {}
 	
 private:
-	void printSharedData();
+	void printSharedData(vector<SharedRAbundVector*>);
 	GlobalData* globaldata;
-	ReadMatrix* read;
+	ReadOTUFile* read;
 	SharedListVector* SharedList;
 	InputData* input;
-	Shared* shared;
-	map<string, SharedRAbundVector*>::iterator it;
+	GroupMap* groupMap;
 	ofstream out;
-	string filename;
+	string filename, fileroot;
+	bool firsttime;
+	map<string, ofstream*> filehandles;
+	map<string, ofstream*>::iterator it3;
 
 };