// ==========================================================================
//                 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
// 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 SEQAN_NAMESPACE_MAIN
{

	//////////////////////////////////////////////////////////////////////////////
	// 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 seqan

#endif
