1 // ==========================================================================
2 //                 SeqAn - The Library for Sequence Analysis
3 // ==========================================================================
4 // Copyright (c) 2006-2010, Knut Reinert, FU Berlin
5 // All rights reserved.
6 //
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8 // modification, are permitted provided that the following conditions are met:
9 //
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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
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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