// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, 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_QGRAM_FIND_H
#define SEQAN_HEADER_INDEX_QGRAM_FIND_H

namespace seqan
{

//////////////////////////////////////////////////////////////////////////////
// QGram finders

    struct FinderQGramLookup_; //Finder that simply looks up the q-gram in the hash table

// the docu is now in index_base.h
    typedef Tag<FinderQGramLookup_> const QGramFindLookup;

//____________________________________________________________________________


    template < typename TText, typename TShapeSpec, typename TSpec >
    struct DefaultFinder<Index<TText, IndexQGram<TShapeSpec, TSpec> > > {
        typedef QGramFindLookup Type;
    };


//////////////////////////////////////////////////////////////////////////////
// _findFirstIndex implementation

    template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
    inline void _findFirstIndex(
        Finder< Index<TText, TSpec>, TSpecFinder > &finder,
        TPattern const &pattern,
        QGramFindLookup const)
    {
        typedef Index<TText, TSpec>                                    TIndex;
        typedef typename Fibre<TIndex, QGramSA>::Type                TSA;
        typedef typename Fibre<TIndex, QGramShape>::Type            TShape;
        typedef typename Fibre<TIndex, QGramDir>::Type                TDir;
        typedef typename Fibre<TIndex, QGramBucketMap>::Type        TBucketMap;
        typedef typename Iterator<TSA const, Standard>::Type        TSAIterator;
        typedef typename Iterator<TPattern const, Standard>::Type    TPatternIterator;

        TIndex &index = haystack(finder);
        indexRequire(index, QGramSADir());

        TSAIterator saIt = begin(indexSA(index), Standard());
        TPatternIterator pIt = begin(pattern, Standard());
        TDir const &dir = indexDir(index);
        TShape &shape = indexShape(index);

        if (IsSameType<TBucketMap, Nothing>::VALUE)
        {
            // hashUpper and patterns shorter than the shape can only be used for
            // direct addressing q-gram indices
            // all codes between hash and hashUpper are from q-grams beginning with the pattern
            finder.range.i1 = saIt + dir[hash(shape, pIt, length(pattern))];
            finder.range.i2 = saIt + dir[hashUpper(shape, pIt, length(pattern))];
        }
        else
        {
            // for bucket map based indices we require the pattern and the shape to have the same length
            // and can look up only a single bucket
            SEQAN_ASSERT_EQ(length(pattern), length(shape));
            typename Size<TDir>::Type bktNo = getBucket(index.bucketMap, hash(shape, pIt));
            finder.range.i1 = saIt + dir[bktNo];
            finder.range.i2 = saIt + dir[bktNo + 1];
        }
    }


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

} //namespace seqan

#endif //#ifndef SEQAN_HEADER_

