X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.h;fp=otuhierarchycommand.h;h=8a2c862cb66398ec1c00e964c627d158fc0d39c0;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h new file mode 100644 index 0000000..8a2c862 --- /dev/null +++ b/otuhierarchycommand.h @@ -0,0 +1,50 @@ +#ifndef OTUHIERARCHYCOMMAND_H +#define OTUHIERARCHYCOMMAND_H +/* + * otuhierarchycommand.h + * Mothur + * + * Created by westcott on 1/19/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "command.hpp" +#include "listvector.hpp" + +//********************************************************************************************************************** + +class OtuHierarchyCommand : public Command { + +public: + OtuHierarchyCommand(string); + OtuHierarchyCommand(); + ~OtuHierarchyCommand(){} + + vector setParameters(); + string getCommandName() { return "otu.hierarchy"; } + string getCommandCategory() { return "OTU-Based Approaches"; } + string getHelpString(); + string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; } + string getDescription() { return "relates OTUs at different distances"; } + + + int execute(); + void help() { m->mothurOut(getHelpString()); } + + +private: + bool abort; + set labels; //holds labels to be used + string label, listFile, outputDir, output; + vector outputNames; + + vector getListVectors(); + +}; + +//********************************************************************************************************************** + +#endif + +