added normalize.shared command

[mothur.git] / normalizesharedcommand.h

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
new file mode 100644 (file)
index 0000000..fcfc727
--- /dev/null
+++ b/normalizesharedcommand.h
@@ -0,0 +1,46 @@
+#ifndef NORMALIZESHAREDCOMMAND_H
+#define NORMALIZESHAREDCOMMAND_H
+
+/*
+ *  normalizesharedcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/15/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+#include "inputdata.h"
+#include "readotu.h"
+#include "sharedrabundvector.h"
+
+class GlobalData;
+
+class NormalizeSharedCommand : public Command {
+
+public:
+       NormalizeSharedCommand(string);
+       ~NormalizeSharedCommand();
+       int execute();
+       void help();
+       
+private:
+       GlobalData* globaldata;
+       ReadOTUFile* read;
+       InputData* input;
+       vector<SharedRAbundVector*> lookup;
+       
+       bool abort, allLines, pickedGroups;
+       set<string> labels; //holds labels to be used
+       string groups, label, outputDir, method;
+       int norm;
+       vector<string> Groups;
+       
+       int normalize(vector<SharedRAbundVector*>&, ofstream&);
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup);
+
+};
+
+#endif
+