X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=0f3e7ef2289b39f9ab4807ccda5cbe179ff51d04;hb=5df1b242d9c2b604eb414da44b28de81d52567d7;hp=b305e9a7d9f3256eef03cac34387caea99f4b4ae;hpb=f5023c911c377e5320c5110c78af98dd8841ef58;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index b305e9a..0f3e7ef 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -26,25 +26,27 @@ class GlobalData;
 class SharedCommand : public Command {
 	
 public:
-	SharedCommand();	
+	SharedCommand(string);	
 	~SharedCommand();
 	int execute();	
 	void help() {}
 	
 private:
 	void printSharedData(vector<SharedRAbundVector*>);
-	void createMisMatchFile();
+	int createMisMatchFile();
+	int readOrderFile();
 	bool isValidGroup(string, vector<string>);
+	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
 	
 	GlobalData* globaldata;
 	ReadOTUFile* read;
 	SharedListVector* SharedList;
 	InputData* input;
 	GroupMap* groupMap;
-	vector<string> groups;
+	vector<string> groups, outputNames, order;
 	ofstream out;
-	string filename, fileroot;
-	bool firsttime;
+	string filename, fileroot, outputDir;
+	bool firsttime, pickedGroups;
 	map<string, ofstream*> filehandles;
 	map<string, ofstream*>::iterator it3;