added read.shared, broke up globaldata a bit

[mothur.git] / readsharedcommand.h

diff --git a/readsharedcommand.h b/readsharedcommand.h
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+++ b/readsharedcommand.h
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+#ifndef READSHAREDCOMMAND_H
+#define READSHAREDCOMMAND_H
+/*
+ *  readsharedcommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 2/12/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+#include <iostream>
+#include <fstream>
+#include "command.hpp"
+#include "readmatrix.hpp"
+#include "inputdata.h"
+
+/* The read.shared must be run before you execute a collect.shared, rarefaction.shared or summary.shared command.
+The read.shared command is used to read a shared file. The read.shared should be entered in the following format:
+read.shared(shared=yourSharedFile). The shared parameter is required.  */
+
+class GlobalData;
+
+class ReadSharedCommand : public Command {
+public:
+       ReadSharedCommand();
+       ~ReadSharedCommand();
+       int execute();
+       
+private:
+       GlobalData* globaldata;
+       ReadMatrix* read;
+       InputData* input;
+       string filename;
+};
+
+#endif
+
+
+
+