Revert to previous commit

[mothur.git] / deuniqueseqscommand.h

diff --git a/deuniqueseqscommand.h b/deuniqueseqscommand.h
new file mode 100644 (file)
index 0000000..300a1ca
--- /dev/null
+++ b/deuniqueseqscommand.h
@@ -0,0 +1,48 @@
+#ifndef DEUNIQUESEQSCOMMAND_H
+#define DEUNIQUESEQSCOMMAND_H
+/*
+ *  deuniqueseqscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 10/19/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+/* This command is the reverse of unique.seqs */ 
+
+class DeUniqueSeqsCommand : public Command {
+
+public:
+       DeUniqueSeqsCommand(string);
+       DeUniqueSeqsCommand();
+       ~DeUniqueSeqsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "deunique.seqs";               }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Deunique.seqs"; }
+       string getDescription()         { return "reverse of the unique.seqs command, and creates a fasta file from a fasta and name file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+
+       string fastaFile, nameFile, outputDir;
+       vector<string> outputNames;
+       bool abort;
+       
+       map<string, string> nameMap;
+       
+       int readNamesFile();
+       
+};
+
+#endif
+