X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mergegroupscommand.h;h=4db344763950b4d53376b3d44e5afebef61db2f8;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=827f5a32762ce7f6d3c11fd0735e64f5e729e7fd;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
index 827f5a3..4db3447 100644
--- a/mergegroupscommand.h
+++ b/mergegroupscommand.h
@@ -24,7 +24,11 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "merge.groups";	}
 	string getCommandCategory()		{ return "General";			}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Merge.groups"; }
+	string getDescription()		{ return "reads shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -35,10 +39,12 @@ private:
 	
 	bool abort, allLines, pickedGroups;
 	set<string> labels; //holds labels to be used
-	string groups, label, outputDir, inputDir, designfile, sharedfile;
+	string groups, label, outputDir, inputDir, designfile, sharedfile, groupfile;
 	vector<string> Groups, outputNames;
 		
 	int process(vector<SharedRAbundVector*>&, ofstream&);
+	int processSharedFile(GroupMap*&);
+	int processGroupFile(GroupMap*&);
 };
 
 #endif