// Clemens Groepl, 2009/2010
// Praxis des Programmierens, WS 2009/10, Uni Greifswald


#ifndef KERNEL_HPP
#define KERNEL_HPP

#include <vector>
#include <istream>
#include <ostream>

/// Representation for an LC-MS feature
class Feature
{
	public:

	/// default constructor, TODO initialize rt mz intens
	Feature ();

	/// copy constructor
	Feature( const Feature& rhs );

	/// destructor, actually not necessary right now
	~Feature();

	/// accessor for retention time
	double getRT() const;

	/// mutator for retention time
	void setRT( double rhs );

	/// TODO DOCME
	double getMZ() const;
	/// TODO DOCME
	void setMZ( double rhs );

	/// TODO DOCME
	double getIntensity() const;
	/// TODO DOCME
	void setIntensity( double rhs );

	/// read a Feature from a stream
	void readStream( std::istream & input );

	/// write a Feature to a stream
	void writeStream( std::ostream & output ) const;

	protected:

		/// retention time
		double rt;
		/// mass-to-charge
		double mz;
		/// intensity
		double intens;

};

/// Representation for a "map" of LC-MS features
class FeatureMap
	: public std::vector<Feature>
{
	public:

	/// read a FeatureMap from a stream
	void readStream( std::istream & input );

	/// write a FeatureMap to a stream
	void writeStream( std::ostream & output ) const;

	/// just an example for what else we might provide in this class
	double getMinRT() const;

};


/// Representation for a collection of features maps
class FeatureMapCollection
	: public std::vector<FeatureMap>
{};

/// An index into a container.  Note that -1 indicates an invalid index.
typedef int Index;

/// Representation for a row of indices (of features within a feature map)
class IndexRow : public std::vector<Index> {};

/// Representation of a table of indices
class IndexMatrix : public std::vector<IndexRow> {};


#endif // KERNEL_HPP