added cluster.classic command

[mothur.git] / clusterdoturcommand.h

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
new file mode 100644 (file)
index 0000000..da2f4a7
--- /dev/null
+++ b/clusterdoturcommand.h
@@ -0,0 +1,52 @@
+#ifndef CLUSTERDOTURCOMMAND_H
+#define CLUSTERDOTURCOMMAND_H
+
+/*
+ *  clusterdoturcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 10/27/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "nameassignment.hpp"
+#include "globaldata.hpp"
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "listvector.hpp"
+
+
+class ClusterDoturCommand : public Command {
+       
+public:
+       ClusterDoturCommand(string);
+       ClusterDoturCommand();
+       ~ClusterDoturCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();  
+       void help();
+       
+private:
+       bool abort, hard;
+       string method, fileroot, tag, outputDir, phylipfile, namefile;
+       double cutoff;
+       int precision, length;
+       ofstream sabundFile, rabundFile, listFile;
+       NameAssignment* nameMap;
+       ListVector* list;
+       RAbundVector* rabund;
+       RAbundVector oldRAbund;
+       ListVector oldList;
+       
+       void printData(string label);
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+};
+
+#endif
+