added merge.groups command

[mothur.git] / mergegroupscommand.h

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
new file mode 100644 (file)
index 0000000..62839ec
--- /dev/null
+++ b/mergegroupscommand.h
@@ -0,0 +1,47 @@
+#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 GlobalData;
+
+class MergeGroupsCommand : public Command {
+       
+public:
+       MergeGroupsCommand(string);
+       MergeGroupsCommand();
+       ~MergeGroupsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();
+       
+private:
+       GlobalData* globaldata;
+       GroupMap* designMap;
+       vector<SharedRAbundVector*> lookup;
+       map<string, vector<string> > outputTypes;
+       
+       bool abort, allLines, pickedGroups;
+       set<string> labels; //holds labels to be used
+       string groups, label, outputDir, inputDir, designfile, sharedfile;
+       vector<string> Groups, outputNames;
+               
+       int process(vector<SharedRAbundVector*>&, ofstream&);
+};
+
+#endif
+