Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
MultiplexFilteringCentroided.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 2002-2015.
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 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERINGCENTROIDED_H
36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERINGCENTROIDED_H
37 
47 
48 #include <vector>
49 #include <algorithm>
50 #include <iostream>
51 
52 namespace OpenMS
53 {
66  class OPENMS_DLLAPI MultiplexFilteringCentroided :
67  public MultiplexFiltering
68  {
69 public:
85  MultiplexFilteringCentroided(const MSExperiment<Peak1D>& exp_picked, const std::vector<MultiplexPeakPattern> patterns, int peaks_per_peptide_min, int peaks_per_peptide_max, bool missing_peaks, double intensity_cutoff, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling);
86 
93  std::vector<MultiplexFilterResult> filter();
94 
95 private:
112  int nonLocalIntensityFilter(MultiplexPeakPattern pattern, int spectrum_index, const std::vector<int>& mz_shifts_actual_indices, std::vector<double>& intensities_actual, int peaks_found_in_all_peptides) const;
113 
124  int getPeakIndex(int spectrum_index, double mz, double scaling) const;
125 
126  };
127 
128 }
129 
130 #endif /* MULTIPLEXFILTERINGCENTROIDED_H_ */
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
filters centroided data for peak patterns
Definition: MultiplexFilteringCentroided.h:66
data structure for pattern of isotopic peaks
Definition: MultiplexPeakPattern.h:54
base class for filtering centroided and profile data for peak patterns
Definition: MultiplexFiltering.h:72

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:26 using doxygen 1.8.9.1