// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2013, 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
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// 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.
//
// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================

#ifndef SEQAN_HEADER_INDEX_FIND_H
#define SEQAN_HEADER_INDEX_FIND_H

namespace SEQAN_NAMESPACE_MAIN
{

//////////////////////////////////////////////////////////////////////////////

	template < typename TText, typename TSpec, typename TSpecFinder >
	struct Position< Finder< Index<TText, TSpec>, TSpecFinder > >:
		SAValue< Index<TText, TSpec> > {};


//////////////////////////////////////////////////////////////////////////////
// generic Finder class for all indices containing a suffix array or 
// similar table, where a query result is an interval in this table
//
// your index must specialize the function _findFirstIndex and set
// finder.range to the interval containing the query hits. See:
//
//	template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
//	inline void _findFirstIndex(
//		Finder< Index<TText, TSpec>, TSpecFinder > &finder,
//		TPattern const &pattern,
//		EsaFindMlr const)
//	{
//		Index<TText, TSpec> &index = haystack(finder);
//		indexRequire(index, EsaSA());
//		finder.range = equalRangeSAIterator(indexText(index), indexSA(index), pattern);
//	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	class Finder< Index<TText, TSpec>, TSpecFinder >
	{
    protected:
		typedef Index<TText, TSpec>								TIndex;
		typedef typename Fibre<TIndex, FibreSA>::Type			TSA;
		typedef typename Iterator<TSA const, Standard>::Type	TIterator;
		typedef typename Size<TIndex>::Type						TSize;

	public:
		Holder<TIndex>	index;
		Pair<TIterator>	range;
		TIterator		data_iterator;
		TSize			data_length;

		Finder() : data_iterator(), data_length(0)
		{
			clear(*this);
		}
		Finder(TIndex &_index): index(_index), data_iterator(), data_length(0)
		{
			clear(*this);
		}
		Finder(TIndex const &_index): index(_index), data_iterator(), data_length(0)
		{
			clear(*this);
		}
	};

//____________________________________________________________________________

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Parameter_< Index<TText, TSpec> >::Type 
	host(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		return value(me.index);
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Parameter_< Index<TText, TSpec> >::Type 
	host(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
	{
SEQAN_CHECKPOINT
		return value(me.index);
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Parameter_< Index<TText, TSpec> >::Type 
	container(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		return value(me.index);
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Parameter_< Index<TText, TSpec> >::Type 
	container(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
	{
SEQAN_CHECKPOINT
		return value(me.index);
	}

//____________________________________________________________________________

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline void
	setHost(
		Finder< Index<TText, TSpec>, TSpecFinder > & me, 
		typename Parameter_<Index<TText, TSpec> >::Type container_)
	{
		me.index = container_;
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline void
	setContainer(
		Finder< Index<TText, TSpec>, TSpecFinder > & me, 
		typename Parameter_<Index<TText, TSpec> >::Type container_)
	{
		me.index = container_;
	}

//____________________________________________________________________________

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Iterator< typename Fibre<Index<TText, TSpec>, FibreSA>::Type const, Standard>::Type &
	hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		return me.data_iterator;
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Iterator< typename Fibre<Index<TText, TSpec>, FibreSA>::Type const, Standard>::Type const &
	hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
	{
SEQAN_CHECKPOINT
		return me.data_iterator;
	}


//____________________________________________________________________________

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline bool
	empty(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		return me.range.i1 == me.range.i2;
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline void
	clear(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		typedef Index<TText, TSpec>								TIndex;
		typedef typename Fibre<TIndex, FibreSA>::Type			TSA;
		typedef typename Iterator<TSA const, Standard>::Type	TIterator;
		me.range.i1 = me.range.i2 = TIterator();
		me.data_length = 0;
	}

//____________________________________________________________________________

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline bool
	atBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		return (empty(me) || hostIterator(me) == me.range.i1);
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline bool
	atEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		return (empty(me) || hostIterator(me) == me.range.i2);
	}

//____________________________________________________________________________

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline void
	goBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		hostIterator(me) = me.range.i1;
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline void
	goEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		hostIterator(me) = me.range.i2;
	}

//____________________________________________________________________________

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
	beginPosition(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
        SEQAN_CHECKPOINT;
		SEQAN_ASSERT_NOT(empty(me));
		return *me.data_iterator;
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
	beginPosition(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
	{
        SEQAN_CHECKPOINT;
		SEQAN_ASSERT_NOT(empty(me));
		return *me.data_iterator;
	}

//____________________________________________________________________________

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
	endPosition(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		return posAdd(beginPosition(me), me.data_length);
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
	endPosition(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
	{
SEQAN_CHECKPOINT
		return posAdd(beginPosition(me), me.data_length);
	}

//____________________________________________________________________________

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
	position(Finder< Index<TText, TSpec>, TSpecFinder > & me)
	{
SEQAN_CHECKPOINT
		return beginPosition(me);
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
	position(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
	{
SEQAN_CHECKPOINT
		return beginPosition(me);
	}

//////////////////////////////////////////////////////////////////////////////
// find

	template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
	inline bool find(
		Finder<Index<TText, TSpec>, TSpecFinder> &finder,
		TPattern const &pattern)
	{
		if (empty(finder)) 
		{
			_findFirstIndex(finder, needle(pattern), TSpecFinder());
			_setFinderLength(finder, length(needle(pattern)));
			hostIterator(finder) = finder.range.i1;
		} else
			++hostIterator(finder);
		return !atEnd(finder);
	}

	template < typename TText, typename TSpec, typename TSpecFinder >
	inline bool find(Finder<Index<TText, TSpec>, TSpecFinder> &finder)
	{
		if (empty(finder)) return false;
		++hostIterator(finder);
		return !atEnd(finder);
	}

}

#endif

