added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / countseqscommand.h

diff --git a/countseqscommand.h b/countseqscommand.h
new file mode 100644 (file)
index 0000000..385cd13
--- /dev/null
+++ b/countseqscommand.h
@@ -0,0 +1,41 @@
+#ifndef COuNTSEQSCOMMAND_H
+#define COuNTSEQSCOMMAND_H
+
+/*
+ *  countseqscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 6/1/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+class CountSeqsCommand : public Command {
+       
+public:
+       
+       CountSeqsCommand(string);
+       CountSeqsCommand();     
+       ~CountSeqsCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "count.seqs";                          }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       string namefile, groupfile, outputDir, groups;
+       bool abort;
+       vector<string> Groups;
+};
+
+#endif
+
+