X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.h;fp=degapseqscommand.h;h=342cd366cd53ce4b8300e2f7d5cd748b04a21668;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/degapseqscommand.h b/degapseqscommand.h
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+#ifndef DEGAPSEQSCOMMAND_H
+#define DEGAPSEQSCOMMAND_H
+
+/*
+ *  degapseqscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 6/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+
+class DegapSeqsCommand : public Command {
+public:
+	DegapSeqsCommand(string);
+	DegapSeqsCommand();
+	~DegapSeqsCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "degap.seqs";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Degap.seqs"; }
+	string getDescription()		{ return "removes gap characters from sequences"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+private:
+
+	bool abort;
+	string fastafile, outputDir;
+	vector<string> outputNames;
+	vector<string> fastaFileNames;
+	
+};
+
+#endif
+