added remove.seqs command

[mothur.git] / removeseqscommand.h

diff --git a/removeseqscommand.h b/removeseqscommand.h
new file mode 100644 (file)
index 0000000..434983e
--- /dev/null
+++ b/removeseqscommand.h
@@ -0,0 +1,38 @@
+#ifndef REMOVESEQSCOMMAND_H
+#define REMOVESEQSCOMMAND_H
+
+/*
+ *  removeseqscommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 7/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+
+class RemoveSeqsCommand : public Command {
+       
+       public:
+       
+               RemoveSeqsCommand(string);      
+               ~RemoveSeqsCommand(){};
+               int execute();
+               void help();    
+               
+       private:
+               set<string> names;
+               string accnosfile, fastafile, namefile, groupfile, alignfile;
+               bool abort;
+               
+               void readFasta();
+               void readName();
+               void readGroup();
+               void readAlign();
+               void readAccnos();
+               
+};
+
+#endif
+