fixed bug with aligner and longest base. added deunique.seqs command.

[mothur.git] / deuniqueseqscommand.h

diff --git a/deuniqueseqscommand.h b/deuniqueseqscommand.h
new file mode 100644 (file)
index 0000000..13176a8
--- /dev/null
+++ b/deuniqueseqscommand.h
@@ -0,0 +1,43 @@
+#ifndef DEUNIQUESEQSCOMMAND_H
+#define DEUNIQUESEQSCOMMAND_H
+/*
+ *  deuniqueseqscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 10/19/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+/* This command is the reverse of unique.seqs */ 
+
+class DeUniqueSeqsCommand : public Command {
+
+public:
+       DeUniqueSeqsCommand(string);
+       DeUniqueSeqsCommand();
+       ~DeUniqueSeqsCommand() {}
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();    
+       
+private:
+
+       string fastaFile, nameFile, outputDir;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       bool abort;
+       
+       map<string, string> nameMap;
+       
+       int readNamesFile();
+       
+};
+
+#endif
+