// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2010, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================

#ifndef SEQAN_HEADER_FRAGMENT_H
#define SEQAN_HEADER_FRAGMENT_H


namespace seqan
{



/**
.Spec.MultiSeed:
..summary:Data structure which represents a seed of multiple sequences.
..cat:Chaining
..cat:Seed Handling
..general:Class.Seed
..signature:Seed<TPosition, MultiSeed>
..param.TPosition:Type of the class which represents the limits (multidimensional point) of a seed.
..include:seqan/chaining.h
*/

////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//
//			Class Seed implementation
//
////////////////////////////////////////////////////////////////////////////////////////////////////////////////

struct MultiSeed;

template <typename TBorder>
class Seed <TBorder, MultiSeed>
{
public:
	typedef MultiSeed TSpec;
	typename Key< Seed< TBorder, TSpec > >::Type * _left;
	typename Key< Seed< TBorder, TSpec > >::Type * _right;
	typename Size< Seed< TBorder, TSpec > >::Type _dim;
	typename Weight< Seed< TBorder, TSpec > >::Type _weight;

/*
#ifdef SEQAN_CHAIN_DEBUG_ // some debugging variables to identify fragments while debugging
	char _id;

	friend inline 
	char 
	_getID( Seed & me )
	{
		return me._id;
	}

	friend inline 
	char 
	_getID( const Seed & me )
	{
		return me._id;
	}

#endif // SEQAN_CHAIN_DEBUG_


#ifdef SEQAN_CHAIN_DEBUG_
	static int _frag_counter;
#endif // SEQAN_CHAIN_DEBUG_
*/

	Seed( )
		: _left( NULL )
		, _right( NULL )
		, _dim( 0 )
		, _weight( 0 )
	{}

	Seed( typename Size< Seed< TBorder, TSpec > >::Type dim )
		: _left( NULL )
		, _right( NULL )
		, _dim( dim )
		, _weight( 0 )
	{
		allocate( *this, _left, _dim );
		allocate( *this, _right, _dim );
	}

	Seed( TBorder * left,
				TBorder * right,
				typename Size< Seed< TBorder, TSpec > >::Type dim )
		: _left( NULL )
		, _right( NULL )
		, _dim( dim )
		, _weight( 0 )
	{
		allocate( *this, _left, _dim );
		allocate( *this, _right, _dim );
		_weight = 0;
		for( typename Size< Seed< TBorder, TSpec > >::Type i = 0; i < dim; ++i )
		{
			_left[ i ] = left[ i ];
			_right[ i ] = right[ i ];
		}
	}

	Seed( TBorder * left,
				TBorder * right,
				typename Size< Seed< TBorder, TSpec > >::Type dim,
				typename Weight< Seed< TBorder, TSpec > >::Type weight )
		: _left( NULL )
		, _right( NULL )
		, _dim( dim )
		, _weight( weight )
	{
		allocate( *this, _left, _dim );
		allocate( *this, _right, _dim );
		for( typename Size< Seed< TBorder, TSpec > >::Type i = 0; i < dim; ++i )
		{
			_left[ i ] = left[ i ];
			_right[ i ] = right[ i ];
		}
	}

	
	Seed & operator=( const Seed & old )
	{
		if( this == &old) 
			return *this;
		if( _left )
			deallocate( *this, _left, _dim );
		if( _right )
			deallocate( *this, _right, _dim );
		_dim = old._dim;
		_weight =  old._weight;
		allocate( *this, _left, _dim );
		allocate( *this, _right, _dim );
		for( typename Size< Seed< TBorder, TSpec > >::Type i = 0; i < _dim; ++i )
		{
			_left[ i ] = old._left[ i ];
			_right[ i ] = old._right[ i ];
		}			
	#ifdef SEQAN_CHAIN_DEBUG_
		_id = old._id;
	#endif
		return *this;
	}

	Seed( const Seed & old )
	{
		_dim = old._dim;
		_weight =  old._weight;
		allocate( *this, _left, _dim );
		allocate( *this, _right, _dim );
		for( typename Size< Seed< TBorder, TSpec > >::Type i = 0; i < _dim; ++i )
		{
			_left[ i ] = old._left[ i ];
			_right[ i ] = old._right[ i ];
		}			
	#ifdef SEQAN_CHAIN_DEBUG_
		_id = old._id;
	#endif
	}

	~Seed()
	{
		deallocate( *this, _left, _dim );
		deallocate( *this, _right, _dim );
		_dim = 0;
		_weight = 0;
	}

	friend inline
	void 
	dump( Seed & me )
	{
		if( me._left != NULL )
		{
			std::cout << "[ ";
			typename Size< Seed< TBorder, TSpec > >::Type dim = 0;
			std::cout << leftPosition( me, dim );
			++dim;
			while( dim != me._dim )
			{
				std::cout << " , " << leftPosition( me, dim );
				++dim;
			}
			std::cout << " ] * [ ";
			dim = 0;
			std::cout << rightPosition( me, dim );
			++dim;
			while( dim != me._dim )
			{
				std::cout << " , "<< rightPosition( me, dim );
				++dim;
			}
			std::cout << " ] "  << weight( me ) << std::endl;
		}
	}

	#ifdef SEQAN_CHAIN_DEBUG_
	friend inline
	void 
	dump( Seed & me, std::ostream & os )
	{
		if( me._left != NULL )
		{
			typename Size< Seed< TBorder, TSpec > >::Type dim = 0;
			os << "# " << weight( me )/10 << std::endl;
			while( dim != me._dim )
			{
				os << "[" << leftPosition( me, dim ) << "," << rightPosition( me, dim ) << "]";
				++dim;
			}
			os << std::endl;
		}
	}
	#endif // SEQAN_CHAIN_DEBUG_

};

template< typename TBorder > inline
typename Size< Seed< TBorder, MultiSeed > >::Type
dimension( Seed< TBorder, MultiSeed > & me )
{
	return me._dim;
}

template< typename TBorder, typename TSize > inline 
TBorder 
leftPosition( Seed< TBorder, MultiSeed >  & me, 
				TSize dim )
{
	return me._left[ dim ];
}

template< typename TBorder, typename TSize > inline 
TBorder 
leftPosition( const Seed< TBorder, MultiSeed >  & me, 
				TSize dim )
{
	return me._left[ dim ];
}

template< typename TBorder, typename TSize > inline 
TBorder 
rightPosition( Seed< TBorder, MultiSeed >  & me, 
				TSize dim )
{
	return me._right[dim];
}

template< typename TBorder, typename TSize > inline 
TBorder 
rightPosition( const Seed< TBorder, MultiSeed >  & me,
				TSize dim )
{
    SEQAN_ASSERT_EQ( me._left->size(), me._right->size());
	return me._right[dim];
}



template< typename TBorder, typename TSpec > inline 
typename Weight< Seed< TBorder, TSpec > >::Type 
weight( Seed< TBorder, TSpec > & me )
{
	return me._weight;
}

template< typename TBorder, typename TSpec > inline 
typename Weight< Seed< TBorder, TSpec > >::Type 
weight( const Seed< TBorder, TSpec > & me )
{
	return me._weight;
}


template< typename TBorder, typename TSpec, typename TWeight > 
inline void 
setWeight( Seed< TBorder, TSpec > & me,
			TWeight weight )
{
	me._weight = weight;
}

template< typename TBorder, typename TSpec, typename TSize, typename TPosition > 
inline void 
_setLeftPosition( Seed< TBorder, TSpec > & me,
					TSize dim,
					TPosition value )
{
	SEQAN_ASSERT_LT_MSG(dim, static_cast<TSize>(me._dim), "Dimension index out of bounds");
	me._left[ dim ] = value;
}
template< typename TPosition, typename TSize, typename TPosition2> 
inline void
setLeftPosition(Seed<TPosition, MultiSeed>  & me, 
				TSize dim,
				TPosition2 new_pos)
{
	_setLeftPosition(me, dim, new_pos);
}

template< typename TBorder, typename TSpec, typename TSize, typename TPosition > 
inline void 
_setRightPosition( Seed< TBorder, TSpec > & me,
					TSize dim, 
					TPosition value )
{
	SEQAN_ASSERT_LT_MSG(dim, static_cast<TSize>(me._dim), "Dimension index out of bounds");
	me._right[ dim ] = value;
}
template< typename TPosition, typename TSize, typename TPosition2> 
inline void 
setRightPosition(Seed<TPosition, MultiSeed>  & me, 
				 TSize dim,
				 TPosition2 new_pos)
{
	_setRightPosition(me, dim, new_pos);
}




//set a fragment to "top" position, that is the starting fragment of a global chain
template <typename TFragment> 
inline void 
makeBeginFragment(TFragment & me)
{
	unsigned int dim = dimension(me);
	for (unsigned int i = 0; i < dim; ++i)
	{
		_setLeftPosition(me, i, 0);		//probably dont need left positions for top fragment
		_setRightPosition(me, i, 0);
	}
}

//set a fragment to "bottom" position in respect to a fragment set
template <typename TFragment, typename TFragments> 
inline void 
makeEndFragment(TFragment & me,
				TFragments & fragments)
{
	typedef typename Size<TFragment>::Type TSize;

	unsigned int dim = dimension(me);
	String<TSize> maxes;
	resize(maxes, dim);
	arrayFill(begin(maxes, Standard()), end(maxes, Standard()), 0);

	typedef typename Iterator<TFragments, Standard>::Type TIterator;
	for (TIterator it = begin(fragments, Standard()); it < end(fragments, Standard()); ++it)
	{
		for (unsigned int i = 0; i < dim; ++i)
		{
			TSize rpos = rightPosition(*it, i);
			if (rpos > maxes[i])
			{
				maxes[i] = rpos;
			}
		}
	}
	for (unsigned int i = 0; i < dim; ++i)
	{
		_setLeftPosition(me, i, maxes[i] );	
		_setRightPosition(me, i, maxes[i] );		//probably dont need right positions for bottom fragments
	}
}




} // namespace seqan

#endif // SEQAN_HEADER_FRAGMENT_H