X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=2c5ab237a2d39b006dee4eca4e9b9b2c65a57ebe;hb=3e2465c16d187247ce3befd29811c2d5dfc15ee8;hp=b305e9a7d9f3256eef03cac34387caea99f4b4ae;hpb=f5023c911c377e5320c5110c78af98dd8841ef58;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index b305e9a..2c5ab23 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -26,25 +26,33 @@ class GlobalData;
 class SharedCommand : public Command {
 	
 public:
-	SharedCommand();	
+	SharedCommand(string);	
+	SharedCommand();
 	~SharedCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
 	void help() {}
 	
 private:
 	void printSharedData(vector<SharedRAbundVector*>);
-	void createMisMatchFile();
+	int createMisMatchFile();
+	int readOrderFile();
 	bool isValidGroup(string, vector<string>);
+	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+	map<string, vector<string> > outputTypes;
 	
 	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;