OpenMS
2.4.0
OpenMS
ANALYSIS
QUANTITATION
QuantitativeExperimentalDesign.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 2002-2018.
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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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// $Authors: Immanuel Luhn$
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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/METADATA/PeptideIdentification.h
>
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#include <
OpenMS/FORMAT/TextFile.h
>
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#include <
OpenMS/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.h
>
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#include <
OpenMS/ANALYSIS/QUANTITATION/ProteinResolver.h
>
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//#include <vector>
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namespace
OpenMS
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{
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class
OPENMS_DLLAPI
QuantitativeExperimentalDesign
:
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public
DefaultParamHandler
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{
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public
:
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QuantitativeExperimentalDesign
();
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//Destructor
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~
QuantitativeExperimentalDesign
()
override
;
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void
applyDesign2Resolver(
ProteinResolver
& resolver,
TextFile
& file,
StringList
& fileNames);
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void
applyDesign2Quantifier(
PeptideAndProteinQuant
& quantifier,
TextFile
& file,
StringList
& fileNames);
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//std::vector< std::pair<PeptideAndProteinQuant::PeptideData,PeptideAndProteinQuant::ProteinQuant> >& result);
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private
:
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QuantitativeExperimentalDesign
(
const
QuantitativeExperimentalDesign
&);
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QuantitativeExperimentalDesign
& operator=(
const
QuantitativeExperimentalDesign
&);
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void
mergeFeatureMaps_(
FeatureMap
& map,
const
String
& experiment,
StringList
& file_paths);
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void
mergeConsensusMaps_(
ConsensusMap
& map,
const
String
& experiment,
StringList
& file_paths);
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void
mergeIDFiles_(std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides,
const
String
& experiment,
StringList
& file_paths);
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void
findRelevantFilePaths_(std::map<String, StringList> & design2FileBaseName, std::map<String, StringList> & design2FilePath,
StringList
& filePaths);
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void
analyzeHeader_(
UInt
& expCol,
UInt
& fileCol,
StringList
& header);
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void
getSeparator_(
String
& separator);
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void
mapFiles2Design_(std::map<String, StringList> & experiments,
TextFile
& file);
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};
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}
// namespace OpenMS
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DefaultParamHandler.h
TextFile.h
OpenMS::String
A more convenient string class.
Definition:
String.h:57
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition:
TextFile.h:46
PeptideAndProteinQuant.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition:
DefaultParamHandler.h:91
OpenMS
Main OpenMS namespace.
Definition:
FeatureDeconvolution.h:46
OpenMS::QuantitativeExperimentalDesign
Merge files according to experimental design.
Definition:
QuantitativeExperimentalDesign.h:56
OpenMS::ConsensusMap
A container for consensus elements.
Definition:
ConsensusMap.h:75
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition:
ListUtils.h:73
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition:
Types.h:94
OpenMS::FeatureMap
A container for features.
Definition:
FeatureMap.h:93
ProteinResolver.h
PeptideIdentification.h
OpenMS::ProteinResolver
Helper class for peptide and protein quantification based on feature data annotated with IDs.
Definition:
ProteinResolver.h:56
OpenMS::PeptideAndProteinQuant
Helper class for peptide and protein quantification based on feature data annotated with IDs.
Definition:
PeptideAndProteinQuant.h:52
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