Revert to previous commit

[mothur.git] / chopseqscommand.h

diff --git a/chopseqscommand.h b/chopseqscommand.h
new file mode 100644 (file)
index 0000000..e73714d
--- /dev/null
+++ b/chopseqscommand.h
@@ -0,0 +1,46 @@
+#ifndef CHOPSEQSCOMMAND_H
+#define CHOPSEQSCOMMAND_H
+
+/*
+ *  chopseqscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 5/10/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "sequence.hpp"
+
+class ChopSeqsCommand : public Command {
+       
+       public:
+       
+               ChopSeqsCommand(string);
+               ChopSeqsCommand();      
+               ~ChopSeqsCommand(){};
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "chop.seqs";           }
+               string getCommandCategory()             { return "Sequence Processing"; }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
+               string getDescription()         { return "trim sequence length"; }
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }          
+       
+       private:
+               string fastafile, outputDir, keep;
+               bool abort, countGaps, Short;
+               int numbases;
+               vector<string> outputNames;
+               
+               string getChopped(Sequence);
+};
+
+#endif
+
+