OpenMS  3.0.0
MultiplexFilteringProfile.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: Lars Nilse $
32 // $Authors: Lars Nilse $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
47 
48 #include <vector>
49 #include <algorithm>
50 #include <iostream>
51 
52 namespace OpenMS
53 {
67  class OPENMS_DLLAPI MultiplexFilteringProfile :
68  public MultiplexFiltering
69  {
70 public:
92  MultiplexFilteringProfile(MSExperiment& exp_profile, const MSExperiment& exp_centroided, const std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& boundaries,
93  const std::vector<MultiplexIsotopicPeakPattern>& patterns, int isotopes_per_peptide_min, int isotopes_per_peptide_max, double intensity_cutoff, double rt_band,
94  double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide");
95 
105  std::vector<MultiplexFilteredMSExperiment> filter();
106 
110  std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& getPeakBoundaries();
111 
112 private:
122  bool filterAveragineModel_(const MultiplexIsotopicPeakPattern& pattern, const MultiplexFilteredPeak& peak, const std::multimap<size_t, MultiplexSatelliteProfile >& satellites_profile) const;
123 
132  bool filterPeptideCorrelation_(const MultiplexIsotopicPeakPattern& pattern, const std::multimap<size_t, MultiplexSatelliteProfile >& satellites_profile) const;
133 
137  std::vector<SplineInterpolatedPeaks> exp_spline_profile_;
138  std::vector<std::vector<PeakPickerHiRes::PeakBoundary> > boundaries_;
139 
140  };
141 
142 }
143 
CubicSpline2d.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::MultiplexIsotopicPeakPattern
data structure for pattern of isotopic peaks
Definition: MultiplexIsotopicPeakPattern.h:54
MultiplexFilteredPeak.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
ProgressLogger.h
BaseFeature.h
MultiplexIsotopicPeakPattern.h
OpenMS::MultiplexFilteringProfile::boundaries_
std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > boundaries_
Definition: MultiplexFilteringProfile.h:138
OpenMS::MultiplexFilteredPeak
data structure storing a single peak that passed all filters
Definition: MultiplexFilteredPeak.h:70
MultiplexFilteredMSExperiment.h
SplineInterpolatedPeaks.h
OpenMS::MultiplexFilteringProfile
filters centroided and profile data for peak patterns
Definition: MultiplexFilteringProfile.h:67
PeakPickerHiRes.h
MultiplexFiltering.h
StandardTypes.h
OpenMS::MultiplexFiltering
base class for filtering centroided and profile data for peak patterns
Definition: MultiplexFiltering.h:73
OpenMS::MultiplexFilteringProfile::exp_spline_profile_
std::vector< SplineInterpolatedPeaks > exp_spline_profile_
spline interpolated profile data and peak boundaries
Definition: MultiplexFilteringProfile.h:137