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[mothur.git] / mergegroupscommand.h

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
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+#ifndef MERGEGROUPSCOMMAND_H
+#define MERGEGROUPSCOMMAND_H
+
+/*
+ *  mergegroupscommand.h
+ *  mothur
+ *
+ *  Created by westcott on 1/24/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "sharedrabundvector.h"
+
+class MergeGroupsCommand : public Command {
+       
+public:
+       MergeGroupsCommand(string);
+       MergeGroupsCommand();
+       ~MergeGroupsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "merge.groups";        }
+       string getCommandCategory()             { return "General";                     }
+       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()); }  
+       
+private:
+       GroupMap* designMap;
+       vector<SharedRAbundVector*> lookup;
+       
+       bool abort, allLines, pickedGroups;
+       set<string> labels; //holds labels to be used
+       string groups, label, outputDir, inputDir, designfile, sharedfile, groupfile;
+       vector<string> Groups, outputNames;
+               
+       int process(vector<SharedRAbundVector*>&, ofstream&);
+       int processSharedFile(GroupMap*&);
+       int processGroupFile(GroupMap*&);
+};
+
+#endif
+