Revert to previous commit

[mothur.git] / degapseqscommand.h

diff --git a/degapseqscommand.h b/degapseqscommand.h
new file mode 100644 (file)
index 0000000..342cd36
--- /dev/null
+++ b/degapseqscommand.h
@@ -0,0 +1,42 @@
+#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
+