X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniqueseqscommand.h;fp=deuniqueseqscommand.h;h=13176a80a413a1bce9d84bb4cf496702a554c446;hb=f09bacac01a842a74c1c1b69070852cc969ff506;hp=0000000000000000000000000000000000000000;hpb=83c530c577250f2bc4c3443b33d97449abf40f36;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> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	int execute();
+	void help();	
+	
+private:
+
+	string fastaFile, nameFile, outputDir;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
+	bool abort;
+	
+	map<string, string> nameMap;
+	
+	int readNamesFile();
+	
+};
+
+#endif
+