X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=2c5ab237a2d39b006dee4eca4e9b9b2c65a57ebe;hb=4116449310d17a847470b84728cdefee5197e67e;hp=f0c24884f05d36f3ed5981ef0ef75a7c57e17a8a;hpb=462fca6d24fd15ca035358ff70bcfae52c3281c3;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index f0c2488..2c5ab23 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -26,22 +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, 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;