added get.lineage and remove.lineage commands

[mothur.git] / getlineagecommand.h

diff --git a/getlineagecommand.h b/getlineagecommand.h
new file mode 100644 (file)
index 0000000..0d07ac6
--- /dev/null
+++ b/getlineagecommand.h
@@ -0,0 +1,40 @@
+#ifndef GETLINEAGECOMMAND_H
+#define GETLINEAGECOMMAND_H
+
+/*
+ *  getlineagecommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/24/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+
+class GetLineageCommand : public Command {
+       
+       public:
+       
+               GetLineageCommand(string);
+               ~GetLineageCommand(){};
+               int execute();
+               void help();    
+               
+       private:
+               set<string> names;
+               vector<string> outputNames;
+               string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+               bool abort, dups;
+               
+               int readFasta();
+               int readName();
+               int readGroup();
+               int readAlign();
+               int readList();
+               int readTax();  
+               string removeConfidences(string);
+};
+
+#endif
+