X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mergegroupscommand.h;h=3e3d337ffa0309f5132d2d88cc3b4c0b81684869;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=dfd65adf1fdc9f7c6c84491f0714eff5cfd3888c;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
index dfd65ad..3e3d337 100644
--- a/mergegroupscommand.h
+++ b/mergegroupscommand.h
@@ -24,8 +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()); }	
@@ -36,10 +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