X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mergegroupscommand.h;h=3e3d337ffa0309f5132d2d88cc3b4c0b81684869;hp=7907dfe85f556682d1cc796323314a2f0c8d7b67;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
index 7907dfe..3e3d337 100644
--- a/mergegroupscommand.h
+++ b/mergegroupscommand.h
@@ -24,7 +24,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "merge.groups";	}
 	string getCommandCategory()		{ return "General";			}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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"; }
 
@@ -38,10 +40,12 @@ 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