1 // ==========================================================================
2 // SeqAn - The Library for Sequence Analysis
3 // ==========================================================================
4 // Copyright (c) 2013 NVIDIA Corporation
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 // Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
33 // ==========================================================================
34
35 #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_
36 #define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_
37
38
39 namespace seqan {
40
41 // --------------------------------------------------------------------------
42 // Dna
43 // --------------------------------------------------------------------------
44
45 template <typename T>
46 inline unsigned char
_translateCharToDna(unsigned char c)47 _translateCharToDna(unsigned char c)
48 {
49 switch (toUpperValue(c))
50 {
51 case 'C':
52 return 1;
53 case 'G':
54 return 2;
55 case 'T':
56 return 3;
57 default:
58 return 0;
59 };
60 }
61
62 // --------------------------------------------------------------------------
63 // Dna5
64 // --------------------------------------------------------------------------
65
66 template <typename T>
67 inline unsigned char
_translateCharToDna5(unsigned char c)68 _translateCharToDna5(unsigned char c)
69 {
70 switch (toUpperValue(c))
71 {
72 case 'A':
73 return 0;
74 case 'C':
75 return 1;
76 case 'G':
77 return 2;
78 case 'T':
79 return 3;
80 default:
81 return 4;
82 };
83 }
84
85 } // namespace seqan
86
87 #endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_
88