X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=0f3e7ef2289b39f9ab4807ccda5cbe179ff51d04;hb=5df1b242d9c2b604eb414da44b28de81d52567d7;hp=20e2ddb3981df57f471970da64e3631814a6c170;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index 20e2ddb..0f3e7ef 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -12,8 +12,7 @@
 #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.  
@@ -27,20 +26,29 @@ class GlobalData;
 class SharedCommand : public Command {
 	
 public:
-	SharedCommand();	
+	SharedCommand(string);	
 	~SharedCommand();
 	int execute();	
+	void help() {}
 	
 private:
-	void printSharedData();
+	void printSharedData(vector<SharedRAbundVector*>);
+	int createMisMatchFile();
+	int readOrderFile();
+	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, order;
 	ofstream out;
-	string filename;
+	string filename, fileroot, outputDir;
+	bool firsttime, pickedGroups;
+	map<string, ofstream*> filehandles;
+	map<string, ofstream*>::iterator it3;
 
 };