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COMPARISON
SPECTRA
SpectrumAlignmentScore.h
Go to the documentation of this file.
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// --------------------------------------------------------------------------
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// OpenMS -- Open-Source Mass Spectrometry
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// --------------------------------------------------------------------------
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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//
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// This software is released under a three-clause BSD license:
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above copyright
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// notice, this list of conditions and the following disclaimer in the
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// documentation and/or other materials provided with the distribution.
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// * Neither the name of any author or any participating institution
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// may be used to endorse or promote products derived from this software
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// without specific prior written permission.
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// For a full list of authors, refer to the file AUTHORS.
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// --------------------------------------------------------------------------
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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// --------------------------------------------------------------------------
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// $Maintainer: Timo Sachsenberg $
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// $Authors: $
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// --------------------------------------------------------------------------
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//
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#pragma once
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#include <
OpenMS/KERNEL/MSSpectrum.h
>
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#include <
OpenMS/KERNEL/Peak1D.h
>
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#include <
OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h
>
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#include <
OpenMS/DATASTRUCTURES/ListUtils.h
>
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#include <
OpenMS/KERNEL/StandardTypes.h
>
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#include <
OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h
>
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#include <boost/math/special_functions/erf.hpp>
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#include <cmath>
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namespace
OpenMS
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{
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class
OPENMS_DLLAPI
SpectrumAlignmentScore
:
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public
PeakSpectrumCompareFunctor
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{
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public
:
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// @name Constructors and Destructors
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// @{
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SpectrumAlignmentScore
();
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SpectrumAlignmentScore
(
const
SpectrumAlignmentScore
& source);
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~
SpectrumAlignmentScore
()
override
;
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// @}
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// @name Operators
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// @{
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SpectrumAlignmentScore
& operator=(
const
SpectrumAlignmentScore
& source);
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double
operator()(
const
PeakSpectrum
& spec1,
const
PeakSpectrum
& spec2)
const override
;
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double
operator()(
const
PeakSpectrum
& spec)
const override
;
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// @}
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// @name Accessors
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// @{
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static
PeakSpectrumCompareFunctor
*
create
() {
return
new
SpectrumAlignmentScore
(); }
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static
const
String
getProductName
()
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{
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return
"SpectrumAlignmentScore"
;
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}
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// @}
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};
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}
OpenMS::String
A more convenient string class.
Definition:
String.h:59
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
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