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
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
|
// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
//
#include <OpenMS/COMPARISON/SPECTRA/BinnedSpectrum.h>
using namespace std;
namespace OpenMS
{
BinnedSpectrum::BinnedSpectrum() :
MSSpectrum<>(), bin_spread_(1), bin_size_(2.0), bins_()
{
}
BinnedSpectrum::BinnedSpectrum(Real size, UInt spread, PeakSpectrum ps) :
MSSpectrum<>(ps), bin_spread_(spread), bin_size_(size), bins_()
{
setBinning();
}
BinnedSpectrum::BinnedSpectrum(const BinnedSpectrum & source) :
MSSpectrum<>(source), bin_spread_(source.getBinSpread()), bin_size_(source.getBinSize()), bins_(source.getBins())
{
}
BinnedSpectrum::~BinnedSpectrum()
{
}
//accessors and operators see .h file
void BinnedSpectrum::setBinning()
{
if (this->MSSpectrum<>::empty())
{
throw BinnedSpectrum::NoSpectrumIntegrated(__FILE__, __LINE__, __PRETTY_FUNCTION__);
}
bins_.clear();
//make all necessary bins accessible
this->sortByPosition();
bins_ = SparseVector<Real>((UInt)ceil(this->back().getMZ() / bin_size_) + bin_spread_, 0, 0);
//put all peaks into bins
UInt bin_number;
for (Size i = 0; i < this->size(); ++i)
{
//bin_number counted form 0 -> floor
bin_number = (UInt)floor(this->operator[](i).getMZ() / bin_size_);
//e.g. bin_size_ = 1.5: first bin covers range [0,1.5] so peak at 1.5 falls in first bin (index 0)
if (this->operator[](i).getMZ() / bin_size_ == (DoubleReal)bin_number)
{
--bin_number;
}
//add peak to corresponding bin
bins_[bin_number] = bins_.at(bin_number) + this->operator[](i).getIntensity();
//add peak to neighboring binspread many
for (Size j = 0; j < bin_spread_; ++j)
{
bins_[bin_number + j + 1] = bins_.at(bin_number + j + 1) + this->operator[](i).getIntensity();
// we are not in one of the first bins (0 to bin_spread)
//not working: if (bin_number-j-1 >= 0)
if (bin_number >= j + 1)
{
bins_[bin_number - j - 1] = bins_.at(bin_number - j - 1) + this->operator[](i).getIntensity();
}
}
}
}
//yields false if given BinnedSpectrum size or spread differs from this one (comparing those might crash)
bool BinnedSpectrum::checkCompliance(const BinnedSpectrum & bs) const
{
return (this->bin_size_ == bs.getBinSize()) &&
(this->bin_spread_ == bs.getBinSpread());
}
BinnedSpectrum::NoSpectrumIntegrated::NoSpectrumIntegrated(const char * file, int line, const char * function, const char * message) throw() :
BaseException(file, line, function, "BinnedSpectrum::NoSpectrumIntegrated", message)
{
}
BinnedSpectrum::NoSpectrumIntegrated::~NoSpectrumIntegrated() throw()
{
}
}
|
