OpenMS  3.0.0
NonNegativeLeastSquaresSolver.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 2002-2022.
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: Chris Bielow $
32 // $Authors: Chris Bielow $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
46  class OPENMS_DLLAPI NonNegativeLeastSquaresSolver
47  {
48 public:
49 
51  {
53  ITERATION_EXCEEDED
54  };
55 
66  static Int solve(const Matrix<double> & A, const Matrix<double> & b, Matrix<double> & x);
67  };
68 
69 } // namespace OpenMS
70 
OpenMS::MSDataWritingConsumer
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:88
LogStream.h
OpenMS::SavitzkyGolayFilter::filterExperiment
void filterExperiment(PeakMap &map)
Removed the noise from an MSExperiment containing profile data.
Definition: SavitzkyGolayFilter.h:214
OpenMS::NonNegativeLeastSquaresSolver::RETURN_STATUS
RETURN_STATUS
Definition: NonNegativeLeastSquaresSolver.h:50
OpenMS::SpectrumSettings::CENTROID
centroid data or stick data
Definition: SpectrumSettings.h:73
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
Size
OpenMS::Exception::IllegalArgument
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::MSChromatogram::isSorted
bool isSorted() const
Checks if all peaks are sorted with respect to ascending RT.
OpenMS::GaussFilter::filterExperiment
void filterExperiment(PeakMap &map)
Smoothes an MSExperiment containing profile data.
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
OpenMS::GaussFilter::filter
void filter(MSSpectrum &spectrum)
Smoothes an MSSpectrum containing profile data.
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Constants::c
const double c
Definition: Constants.h:209
Matrix.h
OpenMS::NonNegativeLeastSquaresSolver
Wrapper for a non-negative least squares (NNLS) solver.
Definition: NonNegativeLeastSquaresSolver.h:46
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
GaussFilter.h
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
SavitzkyGolayFilter.h
OpenMS::Matrix< double >
OpenMS::MSExperiment::getChromatograms
const std::vector< MSChromatogram > & getChromatograms() const
returns the chromatogram list
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::MSExperiment::empty
bool empty() const
Definition: MSExperiment.h:130
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::DataProcessing::SMOOTHING
Smoothing of the signal to reduce noise.
Definition: DataProcessing.h:63
MSExperiment.h
OpenMS::SavitzkyGolayFilter::filter
void filter(InputIt first, InputIt last, OutputIt d_first)
Definition: SavitzkyGolayFilter.h:115
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::MSExperiment::getChromatogram
MSChromatogram & getChromatogram(Size id)
returns a single chromatogram
OpenMS::MzMLFile::transform
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false)
Transforms a map while loading using the supplied MSDataConsumer.
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::SavitzkyGolayFilter
Computes the Savitzky-Golay filter coefficients using QR decomposition.
Definition: SavitzkyGolayFilter.h:101
MSDataWritingConsumer.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::NonNegativeLeastSquaresSolver::SOLVED
Definition: NonNegativeLeastSquaresSolver.h:52
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
OpenMS::GaussFilter
This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform prof...
Definition: GaussFilter.h:70
TOPPBase.h
StringListUtils.h