modified freq parameter be a percentage of numSeqs, added catchall command - not...

[mothur.git] / catchallcommand.h

diff --git a/catchallcommand.h b/catchallcommand.h
new file mode 100644 (file)
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+++ b/catchallcommand.h
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+#ifndef CATCHALLCOMMAND_H
+#define CATCHALLCOMMAND_H
+
+/*
+ *  catchallcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 5/11/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "readotu.h"
+#include "sabundvector.hpp"
+
+/* 
+ citation goes here
+ */ 
+
+/****************************************************************************/
+
+class CatchAllCommand : public Command {
+
+public:
+
+       CatchAllCommand(string);
+       ~CatchAllCommand() {};
+       int execute();
+       void help();    
+       
+private:
+
+       GlobalData* globaldata;
+       ReadOTUFile* read;
+       InputData* input;
+       
+       string outputDir, sabundfile, rabundfile, listfile, format;
+       bool abort, allLines;
+       set<string> labels;
+       
+       string process(SAbundVector*);
+};
+
+/****************************************************************************/
+
+#endif
+
+