added get.otus and remove.otus commands

[mothur.git] / removeotuscommand.h

diff --git a/removeotuscommand.h b/removeotuscommand.h
new file mode 100644 (file)
index 0000000..ce1646b
--- /dev/null
+++ b/removeotuscommand.h
@@ -0,0 +1,50 @@
+#ifndef REMOVEOTUSCOMMAND_H
+#define REMOVEOTUSCOMMAND_H
+
+/*
+ *  removeotuscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/12/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "command.hpp"
+#include "groupmap.h"
+#include "listvector.hpp"
+
+class RemoveOtusCommand : public Command {
+       
+public:
+       
+       RemoveOtusCommand(string);      
+       RemoveOtusCommand();
+       ~RemoveOtusCommand(){}
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();    
+       
+private:
+       string accnosfile, groupfile, listfile, outputDir, groups, label;
+       bool abort;
+       vector<string> outputNames, Groups;
+       map<string, vector<string> > outputTypes;
+       GroupMap* groupMap;
+       
+       void readAccnos();
+       int readListGroup();
+       int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
+       
+};
+
+#endif
+
+
+
+