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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, 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_SHAPE_PREDEFINED_H
#define SEQAN_HEADER_SHAPE_PREDEFINED_H
//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
namespace seqan2
{
//////////////////////////////////////////////////////////////////////////////
// some predefined gapped shapes
//////////////////////////////////////////////////////////////////////////////
// Single seed of
// B.Ma and J.Tromp and M.Li,
// "PatternHunter: faster and more sensitive homology search"
// Bioinformatics 18, 2002
//
// weight:11
// length:18
//
// shape:
// 111010010100110111
typedef GappedShape<
HardwiredShape< 1, 1, 2, 3, 2, 3, 1, 2, 1, 1 >
> ShapePatternHunter;
//////////////////////////////////////////////////////////////////////////////
// Multiple seeds of
// L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
// WABI, 2007
//
// weight:9
// length:15
//
// shapes:
// 111010100100111
// 110100110011101
// 111010001011011
//
// sensitivity:
// 65% 0.747975 70% 0.897741
// 75% 0.973134 80% 0.996226
typedef GappedShape<
HardwiredShape< 1, 1, 2, 2, 3, 3, 1, 1 >
> ShapeIlieA1;
typedef GappedShape<
HardwiredShape< 1, 2, 3, 1, 3, 1, 1, 2 >
> ShapeIlieA2;
typedef GappedShape<
HardwiredShape< 1, 1, 2, 4, 2, 1, 2, 1 >
> ShapeIlieA3;
//////////////////////////////////////////////////////////////////////////////
// Multiple seeds of
// L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
// WABI 2007
//
// weight:9
// length:13..23
//
// shapes:
// 1110110100111
// 11010000110010111
// 11100010010000101011
//
// sensitivity:
// 65% 0.767413 70% 0.910949
// 75% 0.978558 80% 0.997357
typedef GappedShape<
HardwiredShape< 1, 1, 2, 1, 2, 3, 1, 1 >
> ShapeIlieB1;
typedef GappedShape<
HardwiredShape< 1, 2, 5, 1, 3, 2, 1, 1 >
> ShapeIlieB2;
typedef GappedShape<
HardwiredShape< 1, 1, 4, 3, 5, 2, 2, 1 >
> ShapeIlieB3;
} // namespace seqan2
#endif
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