X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removegroupscommand.h;h=c6e9d645c9f7fff26e2c23c634b6264a4614e01b;hp=24062bab3614fb3fc7ee803b3272c4242cdf68bd;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=ecd4f324189cf1cb49a3eb49d5cff58562f27b7f

diff --git a/removegroupscommand.h b/removegroupscommand.h
index 24062ba..c6e9d64 100644
--- a/removegroupscommand.h
+++ b/removegroupscommand.h
@@ -25,7 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "remove.groups";			}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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 +37,7 @@ 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 +50,7 @@ private:
 	int readShared();
 	int readName();
 	int readGroup();
-	void readAccnos();
+    int readCount();
 	int readList();
 	int readTax();
 	int fillNames();