X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=2c5ab237a2d39b006dee4eca4e9b9b2c65a57ebe;hb=4de64268dd8f64b82f3c4e804cac72ffcb6fd583;hp=e5be50a8b9f80488449db640e65721d32f395a5d;hpb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index e5be50a..2c5ab23 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -12,7 +12,6 @@
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "shared.h"
 #include "readotu.h"
 
 /* The shared() command:
@@ -27,22 +26,35 @@ 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();
+	void printSharedData(vector<SharedRAbundVector*>);
+	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;
-	Shared* shared;
-	map<string, SharedRAbundVector*>::iterator it;
-	//vector<SharedRAbundVector*> lookup;
+	GroupMap* groupMap;
+	vector<string> groups, outputNames, order;
 	ofstream out;
-	string filename;
+	string filename, fileroot, outputDir;
+	bool firsttime, pickedGroups;
+	map<string, ofstream*> filehandles;
+	map<string, ofstream*>::iterator it3;
 
 };