X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=a916c854280c74d035968bfc84ec4ab88a4f70e6;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=2c5ab237a2d39b006dee4eca4e9b9b2c65a57ebe;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index 2c5ab23..a916c85 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.  
@@ -21,38 +20,42 @@
 	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();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help() {}
+	
+	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(vector<SharedRAbundVector*>);
-	int createMisMatchFile();
+	void printSharedData(vector<SharedRAbundVector*>, ofstream&);
 	int readOrderFile();
 	bool isValidGroup(string, vector<string>);
 	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
-	map<string, vector<string> > outputTypes;
+	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);
 	
-	GlobalData* globaldata;
-	ReadOTUFile* read;
-	SharedListVector* SharedList;
-	InputData* input;
-	GroupMap* groupMap;
-	vector<string> groups, outputNames, order;
-	ofstream out;
-	string filename, fileroot, outputDir;
-	bool firsttime, pickedGroups;
+	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;