changes while testing

[mothur.git] / mergegroupscommand.h

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
index 827f5a32762ce7f6d3c11fd0735e64f5e729e7fd..3e3d337ffa0309f5132d2d88cc3b4c0b81684869 100644 (file)
--- 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