changed read.shared to read.list and incorporated the shared and parselist commands...

[mothur.git] / readdistcommand.h

diff --git a/readdistcommand.h b/readdistcommand.h
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+#ifndef READDISTCOMMAND_H
+#define READDISTCOMMAND_H
+/*
+ *  readdistcommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 1/20/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include <Carbon/Carbon.h>
+#include <iostream>
+#include <fstream>
+#include "command.hpp"
+#include "readmatrix.hpp"
+
+/* The read.dist command is used to read a distance matrix file.  
+The read.dist command parameter options are phylipfile, columnfile, namefile, cutoff and precision. 
+The read.dist command should be in the following format: read.dist(phylipfile=yourDistFile, 
+namefile=yourNameFile, cutoff=yourCutoff, precision=yourPrecision). The phylipfile or columnfile are required and if you use a columnfile the namefile is required.  
+If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.  */
+
+class NameAssignment;
+class GlobalData;
+
+
+class ReadDistCommand : public Command {
+public:
+       ReadDistCommand();
+       ~ReadDistCommand();
+       int execute();
+       
+private:
+       GlobalData* globaldata;
+       double cutoff;
+       int precision;
+       ReadMatrix* read;
+       string filename, format, method;
+       NameAssignment* nameMap;
+};
+
+#endif
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