1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
|
// ==========================================================================
// Author: Sascha Meiers <meiers@inf.fu-berlin.de>
// ==========================================================================
// Snippets for CyclicShape demonstrations
// ==========================================================================
#include <seqan/sequence.h>
#include <seqan/stream.h> // For printing SeqAn Strings.
#include <seqan/modifier.h>
using namespace seqan2;
int main(int, char const **)
{
{
//![Define FixedCyclicShape]
typedef GappedShape<HardwiredShape<1, 1, 3, 2> > TInnerShape; // 11100101
// ^--You can also use predefied Shapes here, e.g. Patternhunter
typedef CyclicShape<FixedShape<2, TInnerShape, 1> > TShape; // 00111001010
TShape shape;
//![Define FixedCyclicShape]
//![Define FixedCyclicShape Modified String]
typedef ModifiedString<CharString, ModCyclicShape<TShape> > TModString;
CharString str = "das ist das Haus vom Nikolaus";
TModString modStr(str);
std::cout << str << " => " << modStr << std::endl;
//![Define FixedCyclicShape Modified String]
}
{
//![Define GenericCyclicShape]
typedef CyclicShape<GenericShape> TShape;
TShape shape;
stringToCyclicShape(shape, "00111001010");
//![Define GenericCyclicShape]
//![Define GenericCyclicShape Modified String]
typedef ModifiedString<CharString, ModCyclicShape<TShape> > TModString;
CharString str = "das ist das Haus vom Nikolaus";
TModString modStr(str, shape);
std::cout << str << " => " << modStr << std::endl;
//![Define GenericCyclicShape Modified String]
//![Define CyclicShape Modified Iterator]
typedef ModifiedString<CharString, ModCyclicShape<TShape> > TModString;
typedef Iterator<TModString>::Type TModIter;
TModIter it = begin(modStr);
TModIter itBeg = it;
TModIter itEnd = end(modStr);
// output iter position and host iter position
for (; it != itEnd; ++it)
std::cout << (it - itBeg) << "/" << (host(it) - begin(str)) << ", ";
// 0/2, 1/3, 2/4, 3/7, 4/9, 5/13, 6/14, 7/15, 8/18, 9/20, 10/24, 11/25, 12/26,
//![Define CyclicShape Modified Iterator]
//![CyclicShape Care Positions]
std::cout << std::endl << "relative care positions: ";
for (unsigned i = 0; i < weight(shape); ++i)
std::cout << (int)shape.diffs[i] << ","; // output: 1,1,3,2,4,
std::cout << std::endl << "absolute care positions: ";
String<int> carePos;
carePositions(carePos, shape);
for (unsigned i = 0; i < weight(shape); ++i)
std::cout << carePos[i] << ","; // output: 2,3,4,7,9,
std::cout << std::endl;
//![CyclicShape Care Positions]
}
return 0;
}
|
