X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getgroupscommand.h;h=f67c36584a58a14556032ce2374bda17925c6aaa;hp=80230b49b9872ab4633dbd2d4120826b3cc1ee82;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 80230b4..f67c365 100644
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -25,8 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "get.groups";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
 	string getDescription()		{ return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
 
@@ -40,7 +41,7 @@ private:
 	map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
 										   //then the other files need to change the unique name in their file to match.
 										   //only add the names that need to be changed to keep the map search quick
-	string accnosfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
+	string accnosfile, countfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
 	bool abort;
 	vector<string> outputNames, Groups;
 	GroupMap* groupMap;
@@ -48,6 +49,7 @@ private:
 	int readFasta();
 	int readName();
 	int readGroup();
+    int readCount();
 	int readList();
 	int readTax();
 	int fillNames();