X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=861632ce7d6a8026c14b463387b9d8dbb320522d;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=3d39b8b7a54ba348966f80d41cf1cea3b9bc9283;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index 3d39b8b..861632c 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -12,7 +12,6 @@
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "readotu.h"
 
 /* The shared() command:
 	The shared command can only be executed after a successful read.shared command.  
@@ -21,31 +20,39 @@
 	There are no shared command parameters.  The shared command should be in the following format: shared(). */
 
 
-class GlobalData;
-
 class SharedCommand : public Command {
 	
 public:
 	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(vector<SharedRAbundVector*>);
-	void createMisMatchFile();
+	int createMisMatchFile();
+	int readOrderFile();
 	bool isValidGroup(string, vector<string>);
-	void eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+	int ListGroupSameSeqs();
 	
-	GlobalData* globaldata;
-	ReadOTUFile* read;
 	SharedListVector* SharedList;
 	InputData* input;
 	GroupMap* groupMap;
-	vector<string> groups;
+	vector<string> Groups, outputNames, order;
+	set<string> labels;
 	ofstream out;
-	string filename, fileroot, outputDir;
-	bool firsttime, pickedGroups;
+	string filename, fileroot, outputDir, listfile, groupfile, ordergroupfile;
+	bool firsttime, pickedGroups, abort, allLines;
 	map<string, ofstream*> filehandles;
 	map<string, ofstream*>::iterator it3;