added list.seqs command

[mothur.git] / listseqscommand.h

diff --git a/listseqscommand.h b/listseqscommand.h
new file mode 100644 (file)
index 0000000..4e0febd
--- /dev/null
+++ b/listseqscommand.h
@@ -0,0 +1,37 @@
+#ifndef LISTSEQSCOMMAND_H
+#define LISTSEQSCOMMAND_H
+
+/*
+ *  listseqscommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 7/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+class ListSeqsCommand : public Command {
+       
+       public:
+       
+               ListSeqsCommand(string);        
+               ~ListSeqsCommand(){};
+               int execute();
+               void help();    
+               
+       private:
+               vector<string> names;
+               string fastafile, namefile, groupfile, alignfile, inputFileName;
+               bool abort;
+               
+               void readFasta();
+               void readName();
+               void readGroup();
+               void readAlign();
+               
+};
+
+#endif
+