X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.h;h=9d9c194dbbaab4ff7a079058c1c43421937659fe;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=5d0daa2fdc484f55b78613541e1e82ef547a7d09;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/sharedcommand.h b/sharedcommand.h
index 5d0daa2..9d9c194 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -30,6 +30,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "make.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
 	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"; }
@@ -39,7 +40,6 @@ public:
 	
 private:
 	void printSharedData(vector<SharedRAbundVector*>, ofstream&);
-	int createMisMatchFile(SharedListVector*, GroupMap*);
 	int readOrderFile();
 	bool isValidGroup(string, vector<string>);
 	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
@@ -47,13 +47,13 @@ private:
     int createSharedFromListGroup(string);
     int createSharedFromBiom(string);
     string getTag(string&);
-    vector<string> readRows(string, ifstream&, int&); 
+    vector<string> readRows(string, int&); 
     int getDims(string, int&, int&);
-    vector<SharedRAbundVector*> readData(string, string, ifstream&, vector<string>&, 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;
+	string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile, countfile;
 	bool firsttime, pickedGroups, abort, allLines;
 	map<string, ofstream*> filehandles;
 	map<string, ofstream*>::iterator it3;