X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=861632ce7d6a8026c14b463387b9d8dbb320522d;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=08314b56590b70dcb56b29f0c08a454da9ebac5d;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index 08314b5..861632c 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -12,8 +12,6 @@
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "shared.h"
-#include "readotu.h"
 
 /* The shared() command:
 	The shared command can only be executed after a successful read.shared command.  
@@ -22,26 +20,41 @@
 	There are no shared command parameters.  The shared command should be in the following format: shared(). */
 
 
-class GlobalData;
-
 class SharedCommand : public Command {
 	
 public:
-	SharedCommand();	
+	SharedCommand(string);	
+	SharedCommand();
 	~SharedCommand();
-	int execute();	
-	void help() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "make.shared";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
+	string getDescription()		{ return "make a shared file from a list and group file"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	void printSharedData();
-	GlobalData* globaldata;
-	ReadOTUFile* read;
+	void printSharedData(vector<SharedRAbundVector*>);
+	int createMisMatchFile();
+	int readOrderFile();
+	bool isValidGroup(string, vector<string>);
+	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+	int ListGroupSameSeqs();
+	
 	SharedListVector* SharedList;
 	InputData* input;
-	Shared* shared;
-	map<string, SharedRAbundVector*>::iterator it;
+	GroupMap* groupMap;
+	vector<string> Groups, outputNames, order;
+	set<string> labels;
 	ofstream out;
-	string filename;
+	string filename, fileroot, outputDir, listfile, groupfile, ordergroupfile;
+	bool firsttime, pickedGroups, abort, allLines;
+	map<string, ofstream*> filehandles;
+	map<string, ofstream*>::iterator it3;
 
 };