X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedcommand.h;h=39ef9a7a1ebc17f830103cf33d84520aca975f97;hp=1100c3d30afc344119538e89e7c40a8dfa839578;hb=615301e57c25e241356a9c2380648d117709458d;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/sharedcommand.h b/sharedcommand.h
index 1100c3d..39ef9a7 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -30,8 +30,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "make.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	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"; }
 
@@ -40,7 +41,6 @@ public:
 	
 private:
 	void printSharedData(vector<SharedRAbundVector*>, ofstream&);
-	int createMisMatchFile(SharedListVector*, GroupMap*);
 	int readOrderFile();
 	bool isValidGroup(string, vector<string>);
 	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
@@ -48,13 +48,13 @@ 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;