X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=399f3d3966bf828ec32cd790dd0d7d14c7e08c25;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=b3b3e6f5d0381d2354d8113012b13251cdbec7e7;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index b3b3e6f..399f3d3 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -9,14 +9,10 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <map>
 #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.  
@@ -30,20 +26,28 @@ class GlobalData;
 class SharedCommand : public Command {
 	
 public:
-	SharedCommand();	
+	SharedCommand(string);	
 	~SharedCommand();
 	int execute();	
+	void help() {}
 	
 private:
-	void printSharedData();
+	void printSharedData(vector<SharedRAbundVector*>);
+	int createMisMatchFile();
+	bool isValidGroup(string, vector<string>);
+	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+	
 	GlobalData* globaldata;
-	ReadMatrix* read;
+	ReadOTUFile* read;
 	SharedListVector* SharedList;
 	InputData* input;
-	Shared* shared;
-	map<string, SharedRAbundVector*>::iterator it;
+	GroupMap* groupMap;
+	vector<string> groups, outputNames;
 	ofstream out;
-	string filename;
+	string filename, fileroot, outputDir;
+	bool firsttime, pickedGroups;
+	map<string, ofstream*> filehandles;
+	map<string, ofstream*>::iterator it3;
 
 };