X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=phylotypecommand.h;h=ef8b8f17e37051be4951d6dd662d0db1beb1dbaa;hp=0e315ec7c4ef4fcdabc34b4037d7f8bba53cfea2;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hpb=f687723a8357916e86a05116978e6869b039ce36

diff --git a/phylotypecommand.h b/phylotypecommand.h
index 0e315ec..ef8b8f1 100644
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -26,8 +26,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "phylotype";		}
 	string getCommandCategory()		{ return "Clustering";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
 	string getDescription()		{ return "cluster your sequences into OTUs based on their classifications"; }
 
@@ -36,12 +37,11 @@ public:
 	
 private:
 	bool abort, allLines;
-	string taxonomyFileName, label, outputDir, namefile;
+	string taxonomyFileName, label, outputDir, namefile, countfile;
 	set<string> labels; //holds labels to be used
 	int cutoff;
 	map<string, string> namemap;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	map<int, int> currentNodes;
 	map<int, int> parentNodes;