#if !defined(BULLPARSERS_HPP)
#define BULLPARSERS_HPP

#include <string>
#include <vector>

#include "char_encoding.hpp"

namespace bull {

class Tree;

class GetTreesOpts
{
	public:
		GetTreesOpts()
			:storeBrLensFromFile(true),
			fromTree(0),
			toTree(-1)
			{}
			
		bool storeBrLensFromFile;
		std::string filename;
		int fromTree; //index of first tree to store
		int toTree; //index of last tree to get or -1 for all trees
		
		int mode; //paup gettree modes
};

class CodLikeStartOpts
{
};

class SimulateOpts
{
	public:
		SimulateOpts()
			:nReps(1),
			collapsedTreeFilename(),
			concatenations(1),
			overwrite(false),
			paupBlockFilename(),
			outputFilenames()
			{}
			
		
		unsigned nReps; ///# of sim replicates
		std::string collapsedTreeFilename; ///name of file that will store trees that only have internal branches for which there were mutations
		unsigned concatenations; /// # of times (in each replicate) to repeat the "gene" that the model refers to.
		bool overwrite; /// true if output files should be replaced.
		std::vector<std::string> paupBlockFilename;
		std::vector<std::string> outputFilenames; /// datatype to write output in
		std::vector<EncodingType> outTypes; /// datatype to write output in
		std::vector<std::string> treeNames; /// names that the user used to specify the trees
		std::vector<Tree *> treeAlias; ///aliases to the model trees to use
};

} //namespace bull

#endif