X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mergegroupscommand.h;h=3e3d337ffa0309f5132d2d88cc3b4c0b81684869;hp=827f5a32762ce7f6d3c11fd0735e64f5e729e7fd;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
index 827f5a3..3e3d337 100644
--- a/mergegroupscommand.h
+++ b/mergegroupscommand.h
@@ -24,7 +24,12 @@ 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"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -35,10 +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