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SIMULATION
DetectabilitySimulation.h
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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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// $Authors: Stephan Aiche, Chris Bielow$
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// --------------------------------------------------------------------------
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#pragma once
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#include <
OpenMS/DATASTRUCTURES/DefaultParamHandler.h
>
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#include <
OpenMS/SIMULATION/SimTypes.h
>
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namespace
OpenMS
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{
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class
OPENMS_DLLAPI
DetectabilitySimulation
:
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public
DefaultParamHandler
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{
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public
:
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DetectabilitySimulation
();
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DetectabilitySimulation
(
const
DetectabilitySimulation
& source);
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~
DetectabilitySimulation
()
override
;
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DetectabilitySimulation
& operator=(
const
DetectabilitySimulation
& source);
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void
filterDetectability(
SimTypes::FeatureMapSim
& features);
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void
predictDetectabilities(std::vector<String>& peptides_vector, std::vector<double>& labels,
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std::vector<double>& detectabilities);
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private
:
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void
setDefaultParams_();
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void
updateMembers_()
override
;
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double
min_detect_
;
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OpenMS::String
dt_model_file_
;
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protected
:
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void
svmFilter_(
SimTypes::FeatureMapSim
&);
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void
noFilter_(
SimTypes::FeatureMapSim
&);
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};
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}
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DefaultParamHandler.h
SimTypes.h
OpenMS::String
A more convenient string class.
Definition:
String.h:58
OpenMS::DetectabilitySimulation::min_detect_
double min_detect_
Minimum allowed detectability likelihood of a peptide.
Definition:
DetectabilitySimulation.h:94
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition:
DefaultParamHandler.h:91
OpenMS
Main OpenMS namespace.
Definition:
FeatureDeconvolution.h:46
OpenMS::FeatureMap
A container for features.
Definition:
FeatureMap.h:95
OpenMS::DetectabilitySimulation::dt_model_file_
OpenMS::String dt_model_file_
Name of the svm model file.
Definition:
DetectabilitySimulation.h:97
OpenMS::DetectabilitySimulation
Simulates peptide detectability.
Definition:
DetectabilitySimulation.h:52
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