X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removegroupscommand.h;h=c6e9d645c9f7fff26e2c23c634b6264a4614e01b;hp=c6db38057f8c206ecbba0806486078eccdcc7278;hb=615301e57c25e241356a9c2380648d117709458d;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/removegroupscommand.h b/removegroupscommand.h
index c6db380..c6e9d64 100644
--- a/removegroupscommand.h
+++ b/removegroupscommand.h
@@ -25,8 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "remove.groups";			}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	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"; }
 	
@@ -36,7 +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;
@@ -49,6 +50,7 @@ private:
 	int readShared();
 	int readName();
 	int readGroup();
+    int readCount();
 	int readList();
 	int readTax();
 	int fillNames();