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
87
88
89
90
|
/*
Author: Shane Neph
Date: Mon Dec 9 16:07:08 PST 2013
*/
//
// BEDOPS
// Copyright (C) 2011-2022 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License along
// with this program; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
//
#ifndef INTERSECT_REF_VISITOR_HPP
#define INTERSECT_REF_VISITOR_HPP
#include <set>
#include <type_traits>
#include "data/bed/Bed.hpp"
#include "data/bed/BedCompare.hpp"
namespace Visitors {
namespace BedSpecific {
// Collect the total number of overlapping positions
template <
typename Process,
typename BaseVisitor
>
struct EchoMapIntersectLength : BaseVisitor {
typedef BaseVisitor BaseClass;
typedef Process ProcessType;
typedef typename BaseClass::RefType RefType;
typedef typename BaseClass::MapType MapType;
EchoMapIntersectLength(const ProcessType& pt = ProcessType()) : refItem_(0), pt_(pt)
{ /* */ }
inline void SetReference(RefType* t) {
refItem_ = t;
}
inline void Delete(MapType* v) {
win_.erase(v);
}
inline void Add(MapType* v) {
win_.insert(v);
}
inline void DoneReference() {
std::vector<long> vec;
typename SType::const_iterator i = win_.begin();
while ( i != win_.end() ) {
typename std::remove_const<RefType>::type c = *refItem_;
c.intersection(**i++);
vec.push_back(c.length());
} // while
pt_.operator()(vec.begin(), vec.end());
}
virtual ~EchoMapIntersectLength() { }
protected:
typedef Bed::GenomicRestAddressCompare<MapType, MapType> Comp;
typedef std::set<MapType*, Comp> SType;
RefType* refItem_;
ProcessType pt_;
SType win_;
};
} // namespace BedSpecific
} // namespace Visitors
#endif // INTERSECT_REF_VISITOR_HPP
|
