1 | // ==========================================================================
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2 | // SeqAn - The Library for Sequence Analysis
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3 | // ==========================================================================
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4 | // Copyright (c) 2006-2013, Knut Reinert, FU Berlin
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5 | // All rights reserved.
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6 | //
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7 | // Redistribution and use in source and binary forms, with or without
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8 | // modification, are permitted provided that the following conditions are met:
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9 | //
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10 | // * Redistributions of source code must retain the above copyright
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11 | // notice, this list of conditions and the following disclaimer.
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12 | // * Redistributions in binary form must reproduce the above copyright
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13 | // notice, this list of conditions and the following disclaimer in the
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14 | // documentation and/or other materials provided with the distribution.
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15 | // * Neither the name of Knut Reinert or the FU Berlin nor the names of
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16 | // its contributors may be used to endorse or promote products derived
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17 | // from this software without specific prior written permission.
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18 | //
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19 | // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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20 | // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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21 | // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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22 | // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
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23 | // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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24 | // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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25 | // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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26 | // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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27 | // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
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28 | // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
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29 | // DAMAGE.
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30 | //
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31 | // ==========================================================================
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32 | // Author: David Weese <david.weese@fu-berlin.de>
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33 | // ==========================================================================
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34 |
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35 | #ifndef SEQAN_HEADER_SHAPE_PREDEFINED_H
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36 | #define SEQAN_HEADER_SHAPE_PREDEFINED_H
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37 |
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38 | //SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
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39 |
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40 | namespace SEQAN_NAMESPACE_MAIN
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41 | {
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42 |
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43 | //////////////////////////////////////////////////////////////////////////////
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44 | // some predefined gapped shapes
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45 |
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46 |
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47 | //////////////////////////////////////////////////////////////////////////////
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48 | // Single seed of
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49 | // B.Ma and J.Tromp and M.Li,
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50 | // "PatternHunter: faster and more sensitive homology search"
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51 | // Bioinformatics 18, 2002
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52 | //
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53 | // weight:11
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54 | // length:18
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55 | //
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56 | // shape:
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57 | // 111010010100110111
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58 |
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59 | typedef GappedShape<
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60 | HardwiredShape< 1, 1, 2, 3, 2, 3, 1, 2, 1, 1 >
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61 | > ShapePatternHunter;
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62 |
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63 |
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64 |
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65 | //////////////////////////////////////////////////////////////////////////////
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66 | // Multiple seeds of
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67 | // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
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68 | // WABI, 2007
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69 | //
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70 | // weight:9
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71 | // length:15
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72 | //
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73 | // shapes:
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74 | // 111010100100111
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75 | // 110100110011101
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76 | // 111010001011011
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77 | //
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78 | // sensitivity:
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79 | // 65% 0.747975 70% 0.897741
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80 | // 75% 0.973134 80% 0.996226
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81 |
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82 | typedef GappedShape<
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83 | HardwiredShape< 1, 1, 2, 2, 3, 3, 1, 1 >
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84 | > ShapeIlieA1;
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85 |
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86 | typedef GappedShape<
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87 | HardwiredShape< 1, 2, 3, 1, 3, 1, 1, 2 >
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88 | > ShapeIlieA2;
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89 |
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90 | typedef GappedShape<
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91 | HardwiredShape< 1, 1, 2, 4, 2, 1, 2, 1 >
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92 | > ShapeIlieA3;
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93 |
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94 |
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95 |
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96 | //////////////////////////////////////////////////////////////////////////////
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97 | // Multiple seeds of
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98 | // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
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99 | // WABI 2007
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100 | //
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101 | // weight:9
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102 | // length:13..23
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103 | //
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104 | // shapes:
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105 | // 1110110100111
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106 | // 11010000110010111
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107 | // 11100010010000101011
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108 | //
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109 | // sensitivity:
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110 | // 65% 0.767413 70% 0.910949
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111 | // 75% 0.978558 80% 0.997357
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112 |
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113 | typedef GappedShape<
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114 | HardwiredShape< 1, 1, 2, 1, 2, 3, 1, 1 >
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115 | > ShapeIlieB1;
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116 |
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117 | typedef GappedShape<
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118 | HardwiredShape< 1, 2, 5, 1, 3, 2, 1, 1 >
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119 | > ShapeIlieB2;
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120 |
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121 | typedef GappedShape<
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122 | HardwiredShape< 1, 1, 4, 3, 5, 2, 2, 1 >
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123 | > ShapeIlieB3;
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124 |
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125 |
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126 | } // namespace seqan
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127 |
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128 | #endif
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