added phylotype command which reads a taxonomy file and creates a .list, .rabund...

[mothur.git] / phylotypecommand.h

diff --git a/phylotypecommand.h b/phylotypecommand.h
new file mode 100644 (file)
index 0000000..0322daf
--- /dev/null
+++ b/phylotypecommand.h
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+#ifndef PHYLOTYPECOMMAND_H
+#define PHYLOTYPECOMMAND_H
+
+
+/*
+ *  phylotypecommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/20/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "taxonomyequalizer.h"
+#include "command.hpp"
+
+/*************************************************************************/
+
+class PhylotypeCommand : public Command {
+       
+public:
+       PhylotypeCommand(string);       
+       ~PhylotypeCommand();
+       int execute(); 
+       void help();    
+       
+private:
+       bool abort, allLines;
+       string taxonomyFileName, label;
+       set<string> labels; //holds labels to be used
+       int cutoff;
+       
+       map<int, int> currentNodes;
+       map<int, int> parentNodes;
+       map<int, int>::iterator itCurrent;
+
+};
+
+
+/*************************************************************************/
+
+
+#endif
+
+
+