X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removerarecommand.h;h=6a9f2699c6d0a404403372e8ab081d11c9fa85d1;hp=2d70ba784bdf9b413e8726f1cd160f62b85980d7;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/removerarecommand.h b/removerarecommand.h
index 2d70ba7..6a9f269 100644
--- a/removerarecommand.h
+++ b/removerarecommand.h
@@ -26,8 +26,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "remove.rare";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
 	string getDescription()		{ return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
 
@@ -36,7 +37,7 @@ public:
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
+	string sabundfile, rabundfile, sharedfile, groupfile, countfile, listfile, outputDir, groups, label;
 	int nseqs, allLines;
 	bool abort, byGroup;
 	vector<string> outputNames, Groups;
@@ -46,7 +47,7 @@ private:
 	int processRabund();
 	int processList();
 	int processShared();
-	int processLookup(vector<SharedRAbundVector*>&, ofstream&);
+	int processLookup(vector<SharedRAbundVector*>&);
 	
 };