X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniqueseqscommand.h;fp=deuniqueseqscommand.h;h=300a1caeab4ce8b6b2febb10b6082c857fcfeb93;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/deuniqueseqscommand.h b/deuniqueseqscommand.h
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+++ b/deuniqueseqscommand.h
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+#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
+