X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.h;h=c36998ad8bb52349d3c5d0ee73812dd8a6f50c07;hb=5c5c0428f6d548c28a8b903ac80efed4f92d59db;hp=24062bab3614fb3fc7ee803b3272c4242cdf68bd;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/removegroupscommand.h b/removegroupscommand.h
index 24062ba..c36998a 100644
--- a/removegroupscommand.h
+++ b/removegroupscommand.h
@@ -25,6 +25,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "remove.groups";			}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
 	string getDescription()		{ return "removes sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
@@ -35,7 +36,7 @@ public:
 	
 private:
 	set<string> names;
-	string accnosfile, fastafile, namefile, groupfile, designfile, listfile, taxfile, outputDir, groups, sharedfile;
+	string accnosfile, fastafile, namefile, groupfile, countfile, designfile, listfile, taxfile, outputDir, groups, sharedfile;
 	bool abort;
 	vector<string> outputNames, Groups;
 	GroupMap* groupMap;
@@ -48,7 +49,7 @@ private:
 	int readShared();
 	int readName();
 	int readGroup();
-	void readAccnos();
+    int readCount();
 	int readList();
 	int readTax();
 	int fillNames();