X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedcommand.h;h=a916c854280c74d035968bfc84ec4ab88a4f70e6;hp=b3b3e6f5d0381d2354d8113012b13251cdbec7e7;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed

diff --git a/sharedcommand.h b/sharedcommand.h
index b3b3e6f..a916c85 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -9,14 +9,9 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <map>
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
-#include "shared.h"
-#include "readmatrix.hpp"
 
 /* The shared() command:
 	The shared command can only be executed after a successful read.shared command.  
@@ -25,25 +20,44 @@
 	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();	
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "make.shared";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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;
-	ReadMatrix* read;
-	SharedListVector* SharedList;
-	InputData* input;
-	Shared* shared;
-	map<string, SharedRAbundVector*>::iterator it;
-	ofstream out;
-	string filename;
+	void printSharedData(vector<SharedRAbundVector*>, ofstream&);
+	int readOrderFile();
+	bool isValidGroup(string, vector<string>);
+	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+	int ListGroupSameSeqs(vector<string>&, SharedListVector*);
+    int createSharedFromListGroup();
+    int createSharedFromBiom();
+    string getTag(string&);
+    vector<string> readRows(string, int&); 
+    int getDims(string, int&, int&);
+    vector<SharedRAbundVector*> readData(string, string, string, vector<string>&, int);
+	
+	vector<string> Groups, outputNames, order;
+	set<string> labels;
+	string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile, countfile;
+	bool firsttime, pickedGroups, abort, allLines;
+	map<string, ofstream*> filehandles;
+	map<string, ofstream*>::iterator it3;
 
 };