1 // ========================================================================== 2 // SeqAn - The Library for Sequence Analysis 3 // ========================================================================== 4 // Copyright (c) 2006-2010, Knut Reinert, FU Berlin 5 // All rights reserved. 6 // 7 // Redistribution and use in source and binary forms, with or without 8 // modification, are permitted provided that the following conditions are met: 9 // 10 // * Redistributions of source code must retain the above copyright 11 // notice, this list of conditions and the following disclaimer. 12 // * Redistributions in binary form must reproduce the above copyright 13 // notice, this list of conditions and the following disclaimer in the 14 // documentation and/or other materials provided with the distribution. 15 // * Neither the name of Knut Reinert or the FU Berlin nor the names of 16 // its contributors may be used to endorse or promote products derived 17 // from this software without specific prior written permission. 18 // 19 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 20 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 21 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 22 // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE 23 // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 24 // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 25 // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 26 // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 27 // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY 28 // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH 29 // DAMAGE. 30 // 31 // ========================================================================== 32 33 #ifndef SEQAN_HEADER_SEQUENCE_MODEL_TYPES_H 34 #define SEQAN_HEADER_SEQUENCE_MODEL_TYPES_H 35 36 namespace SEQAN_NAMESPACE_MAIN 37 { 38 39 ////////////////////////////////////////////////////////////////////////////// 40 // Tags 41 ////////////////////////////////////////////////////////////////////////////// 42 43 44 /** 45 .Tag.Oops: 46 ..summary:Represents the One Occurrence Per Sequence model. 47 ..cat:Motif Search 48 ..remarks:The @Tag.Oops@ model, which was introduced by Lawrence and Reilly permits 49 exactly one motif occurrence in each sequence. 50 ..include:seqan/find_motif.h 51 */ 52 53 struct Oops 54 { 55 enum{VALUE=0}; 56 }; 57 58 ////////////////////////////////////////////////////////////////////////////// 59 60 /** 61 .Tag.Omops: 62 ..summary:Represents the One or More Occurences Per Sequence model. 63 ..cat:Motif Search 64 ..remarks:The @Tag.Omops@ model is comparable with the @Tag.Tcm@ model with the one difference 65 that zero occurrence in a sample sequence is not permitted. 66 ..include:seqan/find_motif.h 67 */ 68 69 struct Omops 70 { 71 enum{VALUE=1}; 72 }; 73 74 ////////////////////////////////////////////////////////////////////////////// 75 76 /** 77 .Tag.Zoops: 78 ..summary:Represents the Zero or One Occurence Per Sequence model. 79 ..cat:Motif Search 80 ..remarks:The @Tag.Zoops@ model formulated by Bailey and Elkan permits at most one 81 motif occurrence in each sequence. 82 ..include:seqan/find_motif.h 83 */ 84 85 struct Zoops 86 { 87 enum{VALUE=2}; 88 double threshold; 89 ZoopsZoops90 Zoops(): 91 threshold((double)0.5) 92 { 93 } ZoopsZoops94 Zoops(double val): 95 threshold(val) 96 { 97 } ~ZoopsZoops98 ~Zoops() 99 { 100 } 101 }; 102 103 ////////////////////////////////////////////////////////////////////////////// 104 105 /** 106 .Tag.Tcm: 107 ..summary:Represents the Two-Component-Mixture Sequence model. 108 ..cat:Motif Search 109 ..remarks:The @Tag.Tcm@ model formulated by Bailey and Elkan permits any number pf 110 non-overlapping motif occurrences per sequence. 111 ..include:seqan/find_motif.h 112 */ 113 114 struct Tcm 115 { 116 enum{VALUE=3}; 117 double threshold; 118 TcmTcm119 Tcm(): 120 threshold((double)0.5) 121 { 122 } TcmTcm123 Tcm(double val): 124 threshold(val) 125 { 126 } ~TcmTcm127 ~Tcm() 128 { 129 } 130 }; 131 132 ////////////////////////////////////////////////////////////////////////////// 133 134 } // namespace SEQAN_NAMESPACE_MAIN 135 136 #endif //#ifndef SEQAN_HEADER_... 137