| 1 | /*==========================================================================
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| 2 | SeqAn - The Library for Sequence Analysis
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| 3 | http://www.seqan.de
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| 4 | ============================================================================
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| 5 | Copyright (C) 2007
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| 6 |
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| 7 | This library is free software; you can redistribute it and/or
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| 8 | modify it under the terms of the GNU Lesser General Public
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| 9 | License as published by the Free Software Foundation; either
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| 10 | version 3 of the License, or (at your option) any later version.
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| 11 |
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| 12 | This library is distributed in the hope that it will be useful,
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| 13 | but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 14 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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| 15 | Lesser General Public License for more details.
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| 16 |
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| 17 | ============================================================================
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| 18 | $Id: shape_gapped.h 996 2007-08-06 16:38:01Z weese@PCPOOL.MI.FU-BERLIN.DE $
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| 19 | ==========================================================================*/
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| 20 |
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| 21 | #ifndef SEQAN_HEADER_SHAPE_PREDEFINED_H
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| 22 | #define SEQAN_HEADER_SHAPE_PREDEFINED_H
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| 23 |
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| 24 | //SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
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| 25 |
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| 26 | namespace SEQAN_NAMESPACE_MAIN
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| 27 | {
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| 28 |
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| 29 | //////////////////////////////////////////////////////////////////////////////
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| 30 | // some predefined gapped shapes
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| 31 |
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| 32 |
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| 33 | //////////////////////////////////////////////////////////////////////////////
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| 34 | // Single seed of
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| 35 | // B.Ma and J.Tromp and M.Li,
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| 36 | // "PatternHunter: faster and more sensitive homology search"
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| 37 | // Bioinformatics 18, 2002
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| 38 | //
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| 39 | // weight:11
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| 40 | // length:18
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| 41 | //
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| 42 | // shape:
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| 43 | // 111010010100110111
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| 44 |
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| 45 | typedef FixedGappedShape<
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| 46 | HardwiredShape< 1, 1, 2, 3, 2, 3, 1, 2, 1, 1 >
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| 47 | > ShapePatternHunter;
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| 48 |
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| 49 |
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| 50 |
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| 51 | //////////////////////////////////////////////////////////////////////////////
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| 52 | // Multiple seeds of
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| 53 | // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
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| 54 | // WABI, 2007
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| 55 | //
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| 56 | // weight:9
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| 57 | // length:15
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| 58 | //
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| 59 | // shapes:
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| 60 | // 111010100100111
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| 61 | // 110100110011101
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| 62 | // 111010001011011
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| 63 | //
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| 64 | // sensitivity:
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| 65 | // 65% 0.747975 70% 0.897741
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| 66 | // 75% 0.973134 80% 0.996226
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| 67 |
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| 68 | typedef FixedGappedShape<
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| 69 | HardwiredShape< 1, 1, 2, 2, 3, 3, 1, 1 >
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| 70 | > ShapeIlie_9_15_1;
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| 71 |
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| 72 | typedef FixedGappedShape<
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| 73 | HardwiredShape< 1, 2, 3, 1, 3, 1, 1, 2 >
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| 74 | > ShapeIlie_9_15_2;
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| 75 |
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| 76 | typedef FixedGappedShape<
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| 77 | HardwiredShape< 1, 1, 2, 4, 2, 1, 2, 1 >
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| 78 | > ShapeIlie_9_15_3;
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| 79 |
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| 80 |
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| 81 |
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| 82 | //////////////////////////////////////////////////////////////////////////////
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| 83 | // Multiple seeds of
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| 84 | // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
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| 85 | // WABI 2007
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| 86 | //
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| 87 | // weight:9
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| 88 | // length:13..23
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| 89 | //
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| 90 | // shapes:
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| 91 | // 1110110100111
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| 92 | // 11010000110010111
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| 93 | // 11100010010000101011
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| 94 | //
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| 95 | // sensitivity:
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| 96 | // 65% 0.767413 70% 0.910949
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| 97 | // 75% 0.978558 80% 0.997357
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| 98 |
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| 99 | typedef FixedGappedShape<
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| 100 | HardwiredShape< 1, 1, 2, 1, 2, 3, 1, 1 >
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| 101 | > ShapeIlie_9_1323_1;
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| 102 |
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| 103 | typedef FixedGappedShape<
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| 104 | HardwiredShape< 1, 2, 5, 1, 3, 2, 1, 1 >
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| 105 | > ShapeIlie_9_1323_2;
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| 106 |
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| 107 | typedef FixedGappedShape<
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| 108 | HardwiredShape< 1, 1, 4, 3, 5, 2, 2, 1 >
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| 109 | > ShapeIlie_9_1323_3;
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| 110 |
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| 111 |
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| 112 | } // namespace seqan
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| 113 |
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| 114 | #endif
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