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3D
OpenMS/OpenMS
doc/code_examples/ExamplePlugin.py
.py
2,277
61
#!/usr/bin/env python import argparse from pyopenms import Param, ParamXMLFile, MSExperiment, MzMLFile ''' The tool needs basic parameter parsing. The following parameters are required to be supported: -write_ini <filename> : create the ini file for the tool -ini <filename> : the ini file to load -in <filename> : the...
Python
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_FileIO_mzML.cpp
.cpp
1,097
35
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <OpenMS/FORMAT/IndexedMzMLFileLoader.h> #include <OpenMS/KERNEL/OnDiscMSExperiment.h> #include <OpenMS/SYSTEM/File.h> #include <OpenMS/openms_data_path.h> // exotic header for pat...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_Residue.cpp
.cpp
1,305
48
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // //! [doxygen_snippet_Residue] #include <OpenMS/CHEMISTRY/ResidueDB.h> #include <OpenMS/CHEMISTRY/Residue.h> #include <OpenMS/CHEMISTRY/AASequence.h> #include <iostream> using namespace O...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_Clustering.cpp
.cpp
2,578
76
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <OpenMS/ML/CLUSTERING/ClusterAnalyzer.h> #include <OpenMS/ML/CLUSTERING/ClusterHierarchical.h> #include <OpenMS/ML/CLUSTERING/CompleteLinkage.h> #include <OpenMS/ML/CLUSTERING/Sin...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_AASequence.cpp
.cpp
2,340
58
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // //! [doxygen_snippet_AASequence] // This script calculates the mass-to-charge ratio of a 2+ charged b-ion and full peptide from a hardcoded sequence. #include <OpenMS/CHEMISTRY/AASequenc...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_MSChromatogram.cpp
.cpp
864
36
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause //! [doxygen_snippet_MSChromatogram] #include <OpenMS/KERNEL/ChromatogramPeak.h> #include <OpenMS/KERNEL/MSChromatogram.h> #include <OpenMS/METADATA/ChromatogramSettings.h> using namespace ...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_TOPP.cpp
.cpp
5,857
176
//! [doxygen_snippet_TOPPexample] // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // -------------------------------------------------------------------------- // $Maintainer: Oliver Alka $ // $Authors: Oliver Alka $ // This file is ONLY us...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_TheoreticalSpectrumGenerator.cpp
.cpp
1,780
57
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // //! [doxygen_snippet_TSG] #include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h> #include <OpenMS/CHEMISTRY/AASequence.h> #include <OpenMS/KERNEL/MSSpectrum.h> #include <OpenMS/KERNEL...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_FileIO_Consumer.cpp
.cpp
1,663
49
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <OpenMS/FORMAT/MzMLFile.h> #include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h> #include <OpenMS/SYSTEM/File.h> #include <OpenMS/openms_data_path.h> // exotic header for pa...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_MorphologicalFilter.cpp
.cpp
934
34
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <OpenMS/PROCESSING/BASELINE/MorphologicalFilter.h> #include <OpenMS/FORMAT/FileHandler.h> #include <OpenMS/KERNEL/StandardTypes.h> #include <OpenMS/openms_data_path.h> // exotic h...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_Element.cpp
.cpp
2,385
64
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // //! [doxygen_snippet_Element] #include <OpenMS/CHEMISTRY/Element.h> #include <OpenMS/CHEMISTRY/ElementDB.h> #include <OpenMS/DATASTRUCTURES/StringListUtils.h> #include <iostream> #include...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_MSSpectrum.cpp
.cpp
1,121
44
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Petra Gutenbrunner $ // $Authors: Petra Gutenbrunner $ // -------------------------------------...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_GaussFilter.cpp
.cpp
861
33
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <OpenMS/PROCESSING/SMOOTHING/GaussFilter.h> #include <OpenMS/FORMAT/FileHandler.h> #include <OpenMS/KERNEL/StandardTypes.h> #include <OpenMS/KERNEL/MSExperiment.h> #include <OpenM...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_FeatureFinder.cpp
.cpp
601
25
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <OpenMS/FEATUREFINDER/FeatureFinderAlgorithmPicked.h> using namespace OpenMS; using namespace std; Int main() { FeatureFinderAlgorithmPicked ff; // ... set parameters (e.g. ...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_DRange.cpp
.cpp
1,475
39
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <OpenMS/DATASTRUCTURES/DRange.h> #include <iostream> using namespace OpenMS; Int main() { // A D-dimensional range, without units; // Note: if you want something more modern...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_RangeManager.cpp
.cpp
809
34
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <OpenMS/KERNEL/FeatureMap.h> #include <iostream> using namespace OpenMS; using namespace std; Int main() { FeatureMap map; Feature feature; feature.setIntensity(461.3f); ...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_GUI_ListEditor.cpp
.cpp
357
18
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <QApplication> #include <OpenMS/VISUAL/ListEditor.h> using namespace OpenMS; int main(int argc, char ** argv) { QApplication app(argc, argv); ListEditor listeditor; listed...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_Labeled.cpp
.cpp
1,216
34
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <OpenMS/CONCEPT/Types.h> #include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmLabeled.h> #include <OpenMS/FORMAT/FileHandler.h> #include <OpenMS/openms_data_path.h> // e...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_Enzyme.cpp
.cpp
1,742
62
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // //! [doxygen_snippet_Enzyme] #include <OpenMS/CHEMISTRY/AASequence.h> #include <OpenMS/CHEMISTRY/ProteaseDigestion.h> #include <vector> #include <iostream> using namespace OpenMS; using...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_EmpiricalFormula.cpp
.cpp
1,246
42
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // //! [doxygen_snippet_EmpiricalFormula] #include <OpenMS/CHEMISTRY/EmpiricalFormula.h> #include <OpenMS/CHEMISTRY/ElementDB.h> #include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopeP...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_IdentificationClasses.cpp
.cpp
4,285
128
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Petra Gutenbrunner $ // $Authors: Petra Gutenbrunner $ // -------------------------------------...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_Logger.cpp
.cpp
1,451
46
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Chris Bielow $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
doc/code_examples/Tutorial_Param.cpp
.cpp
809
28
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // #include <OpenMS/CONCEPT/Types.h> #include <OpenMS/DATASTRUCTURES/Param.h> #include <iostream> using namespace OpenMS; using namespace std; Int main() { Param param; param.setValue(...
C++
3D
OpenMS/OpenMS
doc/doxygen/parameters/TOPPDocumenter.cpp
.cpp
10,954
321
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Marc Sturm, Mathias Walzer, Chris Bielow $ // ---------------------...
C++
3D
OpenMS/OpenMS
doc/doxygen/parameters/DefaultParamHandlerDocumenter.cpp
.cpp
20,032
482
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: $ // $Authors: Marc Sturm $ // ----------------------------------------------------------------...
C++
3D
OpenMS/OpenMS
doc/doxygen/test/Doxygen_Warning_Checker.cpp
.cpp
2,282
64
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Chris Bielow $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/QCExtractor.cpp
.cpp
5,950
170
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Mathias Walzer $ // $Author: Mathias Walzer $ // ----------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/QCEmbedder.cpp
.cpp
9,899
272
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Mathias Walzer $ // $Author: Mathias Walzer $ // ----------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/QCMerger.cpp
.cpp
7,383
206
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Mathias Walzer $ // $Author: Mathias Walzer $ // ----------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/ImageCreator.cpp
.cpp
15,071
416
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Clemens Groepl, Timo Sachsenberg$ // --------------------------...
C++
3D
OpenMS/OpenMS
src/topp/MzMLSplitter.cpp
.cpp
6,576
189
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Hendrik Weisser $ // -------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/StaticModification.cpp
.cpp
8,150
216
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Chris Bielow $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/FileInfo.cpp
.cpp
88,950
2,312
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Lars Nilse $ // $Authors: Marc Sturm, Clemens Groepl, Lars Nilse, Chris Bielow $ // -----------...
C++
3D
OpenMS/OpenMS
src/topp/MapStatistics.cpp
.cpp
18,763
505
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Oliver Kohlbacher $ // $Authors: Oliver Kohlbacher $ // ---------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/GNPSExport.cpp
.cpp
10,224
175
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Dorrestein Lab - University of California San Diego - https://dorresteinlab.ucsd.edu/$ // $Auth...
C++
3D
OpenMS/OpenMS
src/topp/ProteinInference.cpp
.cpp
11,953
294
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Julianus Pfeuffer $ // $Authors: Andreas Bertsch, Julianus Pfeuffer $ // ----------------------...
C++
3D
OpenMS/OpenMS
src/topp/HighResPrecursorMassCorrector.cpp
.cpp
10,852
215
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Timo Sachsenberg, Oliver Alka $ // ----------------------------...
C++
3D
OpenMS/OpenMS
src/topp/EICExtractor.cpp
.cpp
21,279
526
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Chris Bielow $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/ProteinQuantifier.cpp
.cpp
47,453
1,111
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Hendrik Weisser $ // -------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/SiriusExport.cpp
.cpp
6,294
139
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Axel Walter, Oliver Alka $ // $Authors: Axel Walter, Oliver Alka, Timo Sachsenberg $ // -------...
C++
3D
OpenMS/OpenMS
src/topp/OpenSwathConfidenceScoring.cpp
.cpp
8,771
192
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Hannes Roest, Hendrik Weisser $ // -----------------------------...
C++
3D
OpenMS/OpenMS
src/topp/TICCalculator.cpp
.cpp
14,319
421
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hannes Roest $ // $Authors: Hannes Roest $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/MetaboliteAdductDecharger.cpp
.cpp
6,986
179
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Fabian Aicheler $ // $Authors: Fabian Aicheler $ // -------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/QCExporter.cpp
.cpp
7,524
207
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Mathias Walzer $ // $Author: Mathias Walzer $ // ----------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/IDMapper.cpp
.cpp
13,540
250
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Marc Sturm, Hendrik Weisser $ // ------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/Digestor.cpp
.cpp
11,266
293
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Nico Pfeifer, Chris Bielow $ // -----------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/OpenSwathMzMLFileCacher.cpp
.cpp
10,408
300
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hannes Roest $ // $Authors: Hannes Roest $ // ------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/JSONExporter.cpp
.cpp
2,266
89
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Hendrik Weisser $ // -------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/IsobaricAnalyzer.cpp
.cpp
13,487
280
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Chris Bielow $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/IDConflictResolver.cpp
.cpp
5,200
139
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Hendrik Weisser, Lucia Espona $ // -----------------------------...
C++
3D
OpenMS/OpenMS
src/topp/FeatureFinderCentroided.cpp
.cpp
12,656
366
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Clemens Groepl, Marc Sturm $ // ------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/MapNormalizer.cpp
.cpp
4,153
152
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: $ // $Authors: Marc Sturm $ // ----------------------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/ProteomicsLFQ.cpp
.cpp
78,877
1,830
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Timo Sachsenberg $ // ---------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/PeakPickerHiRes.cpp
.cpp
8,820
271
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Eva Lange $ // ------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/MRMPairFinder.cpp
.cpp
12,275
314
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Andreas Bertsch $ // ------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/FeatureLinkerLabeled.cpp
.cpp
3,436
100
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Marc Sturm, Clemens Groepl, Steffen Sass $ // -----------------...
C++
3D
OpenMS/OpenMS
src/topp/FeatureLinkerBase.cpp
.cpp
12,092
354
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Marc Sturm, Clemens Groepl, Steffen Sass $ // -----------------...
C++
3D
OpenMS/OpenMS
src/topp/FeatureFinderLFQ.cpp
.cpp
8,489
214
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Mark Ivanov, Timo Sachsenberg $ // ----------------------------...
C++
3D
OpenMS/OpenMS
src/topp/DatabaseSuitability.cpp
.cpp
14,237
297
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Tom Waschischeck $ // $Authors: Tom Waschischeck $ // -----------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/CVInspector.cpp
.cpp
17,366
425
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Marc Sturm $ // -----------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/FLASHDeconv.cpp
.cpp
20,879
444
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Kyowon Jeong, Jihyung Kim $ // $Authors: Kyowon Jeong, Jihyung Kim $ // -----------------------...
C++
3D
OpenMS/OpenMS
src/topp/FeatureFinderMetabo.cpp
.cpp
18,477
473
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Erhan Kenar, Holger Franken $ // ------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/FileFilter.cpp
.cpp
74,415
1,604
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Marc Sturm, Lars Nilse, Chris Bielow, Hendrik Brauer $ // ---------...
C++
3D
OpenMS/OpenMS
src/topp/PhosphoScoring.cpp
.cpp
11,731
327
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg, Petra Gutenbrunner $ // $Authors: David Wojnar, Timo Sachsenberg, Petra Guten...
C++
3D
OpenMS/OpenMS
src/topp/DTAExtractor.cpp
.cpp
5,754
196
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Marc Sturm $ // -----------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/MetaProSIP.cpp
.cpp
146,874
3,636
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Timo Sachsenberg $ // -----------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/SimpleSearchEngine.cpp
.cpp
4,412
134
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Timo Sachsenberg $ // -----------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/FeatureFinderMetaboIdent.cpp
.cpp
15,949
370
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Hendrik Weisser $ // -------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/IDExtractor.cpp
.cpp
9,339
244
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Nico Pfeifer $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/IDScoreSwitcher.cpp
.cpp
4,403
112
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Hendrik Weisser $ // -------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/IDRipper.cpp
.cpp
6,328
162
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg$ // $Authors: Immanuel Luhn, Leon Kuchenbecker$ // ---------------------------...
C++
3D
OpenMS/OpenMS
src/topp/TargetedFileConverter.cpp
.cpp
8,008
226
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hannes Roest $ // $Authors: George Rosenberger, Hannes Roest $ // -----------------------------...
C++
3D
OpenMS/OpenMS
src/topp/IDRTCalibration.cpp
.cpp
6,867
172
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: $ // ----------------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/IonMobilityBinning.cpp
.cpp
6,589
178
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Chris Bielow $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/OpenSwathFileSplitter.cpp
.cpp
4,939
136
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hannes Roest $ // $Authors: Hannes Roest $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/QCCalculator.cpp
.cpp
8,709
185
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Mathias Walzer, Axel Walter $ // $Author: Mathias Walzer, Sven Nahnsen $ // -------------------...
C++
3D
OpenMS/OpenMS
src/topp/MRMMapper.cpp
.cpp
5,540
163
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hannes Roest $ // $Authors: Hannes Roest $ // ------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/RNAMassCalculator.cpp
.cpp
12,162
331
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Hendrik Weisser $ // -------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/AssayGeneratorMetaboSirius.cpp
.cpp
18,762
359
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Oliver Alka, Axel Walter $ // $Authors: Oliver Alka, Axel Walter $ // -------------------------...
C++
3D
OpenMS/OpenMS
src/topp/MassTraceExtractor.cpp
.cpp
13,500
379
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Erhan Kenar, Holger Franken $ // ------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/FuzzyDiff.cpp
.cpp
7,795
219
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: $ // ----------------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/MapRTTransformer.cpp
.cpp
9,352
214
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Marc Sturm, Clemens Groepl, Hendrik Weisser $ // ---------------...
C++
3D
OpenMS/OpenMS
src/topp/ClusterMassTracesByPrecursor.cpp
.cpp
16,272
397
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hannes Roest $ // $Authors: Hannes Roest $ // ------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/ExecutePipeline.cpp
.cpp
6,354
184
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Johannes Veit $ // $Authors: Johannes Junker, Chris Bielow $ // -------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/MapAlignerIdentification.cpp
.cpp
22,463
555
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Marc Sturm, Clemens Groepl, Hendrik Weisser $ // ---------------...
C++
3D
OpenMS/OpenMS
src/topp/OpenSwathFeatureXMLToTSV.cpp
.cpp
16,749
501
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hannes Roest $ // $Authors: Hannes Roest $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/XFDR.cpp
.cpp
8,989
264
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Eugen Netz $ // $Authors: Lukas Zimmermann, Eugen Netz $ // -----------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/AccurateMassSearch.cpp
.cpp
8,283
225
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Erhan Kenar, Chris Bielow $ // --------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/IDMerger.cpp
.cpp
19,400
484
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Hendrik Weisser $ // ------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/SpectraFilterWindowMower.cpp
.cpp
3,906
133
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Mathias Walzer$ // $Authors: $ // -------------------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/NoiseFilterGaussian.cpp
.cpp
7,452
239
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Eva Lange $ // ------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/IDSplitter.cpp
.cpp
5,785
169
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Hendrik Weisser $ // -------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/PeptideDataBaseSearchFI.cpp
.cpp
4,719
128
// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: $ // $Authors: $ // ---------------------------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/FeatureLinkerUnlabeledQT.cpp
.cpp
3,718
110
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Marc Sturm, Clemens Groepl, Steffen Sass $ // -----------------...
C++
3D
OpenMS/OpenMS
src/topp/IDFileConverter.cpp
.cpp
33,684
808
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Timo Sachsenberg $ // $Authors: Katharina Albers, Clemens Groepl, Chris Bielow, Mathias Walzer,...
C++
3D
OpenMS/OpenMS
src/topp/MultiplexResolver.cpp
.cpp
25,683
624
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Lars Nilse $ // $Authors: Lars Nilse $ // -----------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/OpenSwathDecoyGenerator.cpp
.cpp
17,903
391
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: George Rosenberger $ // $Authors: George Rosenberger, Hannes Roest, Witold Wolski $ // --------...
C++
3D
OpenMS/OpenMS
src/topp/PeptideIndexer.cpp
.cpp
8,536
205
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Andreas Bertsch, Chris Bielow, Knut Reinert $ // ------------------...
C++
3D
OpenMS/OpenMS
src/topp/GenericWrapper.cpp
.cpp
22,655
564
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Chris Bielow $ // $Authors: Chris Bielow $ // -------------------------------------------------...
C++
3D
OpenMS/OpenMS
src/topp/MassCalculator.cpp
.cpp
10,537
298
// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin // SPDX-License-Identifier: BSD-3-Clause // // -------------------------------------------------------------------------- // $Maintainer: Hendrik Weisser $ // $Authors: Hendrik Weisser, Chris Bielow $ // -----------------------------...
C++