OpenMS
2.5.0
Main Page
Related Pages
Modules
Namespaces
Classes
Files
File List
File Members
OpenMS
COMPARISON
SPECTRA
SpectrumAlignmentScore.h
Go to the documentation of this file.
1
// --------------------------------------------------------------------------
2
// OpenMS -- Open-Source Mass Spectrometry
3
// --------------------------------------------------------------------------
4
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6
//
7
// This software is released under a three-clause BSD license:
8
// * Redistributions of source code must retain the above copyright
9
// notice, this list of conditions and the following disclaimer.
10
// * Redistributions in binary form must reproduce the above copyright
11
// notice, this list of conditions and the following disclaimer in the
12
// documentation and/or other materials provided with the distribution.
13
// * Neither the name of any author or any participating institution
14
// may be used to endorse or promote products derived from this software
15
// without specific prior written permission.
16
// For a full list of authors, refer to the file AUTHORS.
17
// --------------------------------------------------------------------------
18
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29
//
30
// --------------------------------------------------------------------------
31
// $Maintainer: Timo Sachsenberg $
32
// $Authors: $
33
// --------------------------------------------------------------------------
34
//
35
#pragma once
36
37
#include <
OpenMS/KERNEL/MSSpectrum.h
>
38
#include <
OpenMS/KERNEL/Peak1D.h
>
39
#include <
OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h
>
40
#include <
OpenMS/DATASTRUCTURES/ListUtils.h
>
41
#include <
OpenMS/KERNEL/StandardTypes.h
>
42
#include <
OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h
>
43
44
#include <boost/math/special_functions/erf.hpp>
45
#include <cmath>
46
47
namespace
OpenMS
48
{
49
69
class
OPENMS_DLLAPI
SpectrumAlignmentScore
:
70
public
PeakSpectrumCompareFunctor
71
{
72
public
:
73
74
// @name Constructors and Destructors
75
// @{
77
SpectrumAlignmentScore
();
78
80
SpectrumAlignmentScore
(
const
SpectrumAlignmentScore
& source);
81
83
~
SpectrumAlignmentScore
()
override
;
84
// @}
85
86
// @name Operators
87
// @{
89
SpectrumAlignmentScore
& operator=(
const
SpectrumAlignmentScore
& source);
90
92
double
operator()(
const
PeakSpectrum
& spec1,
const
PeakSpectrum
& spec2)
const override
;
93
94
double
operator()(
const
PeakSpectrum
& spec)
const override
;
95
// @}
96
97
// @name Accessors
98
// @{
100
static
PeakSpectrumCompareFunctor
*
create
() {
return
new
SpectrumAlignmentScore
(); }
101
103
static
const
String
getProductName
()
104
{
105
return
"SpectrumAlignmentScore"
;
106
}
107
108
// @}
109
110
};
111
112
}
OpenMS::String
A more convenient string class.
Definition:
String.h:58
Peak1D.h
OpenMS::SpectrumAlignmentScore::getProductName
static const String getProductName()
Definition:
SpectrumAlignmentScore.h:103
OpenMS::PeakSpectrumCompareFunctor
Base class for compare functors of spectra, that return a similarity value for two spectra.
Definition:
PeakSpectrumCompareFunctor.h:52
ListUtils.h
OpenMS
Main OpenMS namespace.
Definition:
FeatureDeconvolution.h:46
PeakSpectrumCompareFunctor.h
OpenMS::SpectrumAlignmentScore
Similarity score via spectra alignment.
Definition:
SpectrumAlignmentScore.h:69
OpenMS::SpectrumAlignmentScore::create
static PeakSpectrumCompareFunctor * create()
Definition:
SpectrumAlignmentScore.h:100
SpectrumAlignment.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition:
MSSpectrum.h:67
StandardTypes.h
MSSpectrum.h
Generated on Sat Mar 7 2020 03:23:42 for OpenMS by
1.8.16