OpenMS  2.8.0
FeatureFinderAlgorithmIsotopeWavelet.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 2002-2021.
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: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
61  {
62 public:
63 
65  typedef Peak1D PeakType;
66 
69 
72 
74 
76  void run() override;
77 
78  static const String getProductName();
79 
81 
82 protected:
83 
85  struct BoxElement
86  {
87  double mz;
88  UInt c;
89  double score;
90  double intens;
91  double RT;
92  };
93 
94  typedef std::map<UInt, BoxElement> Box;
95 
98  UInt RT_votes_cutoff_, real_RT_votes_cutoff_, RT_interleave_;
99  String use_gpus_, intensity_type_;
100  bool check_PPMs_, hr_data_;
101  std::vector<UInt> gpu_ids_;
102 
104 
105  void updateMembers_() override;
106 
107  };
108 
109 } //namespace
110 
Implements the isotope wavelet feature finder.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:61
Int progress_counter_
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:103
String intensity_type_
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:99
UInt max_charge_
The maximal charge state we will consider.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:96
MSSpectrum * createHRData(const UInt i)
FeatureFinderAlgorithmIsotopeWavelet()
Default Constructor.
double score
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:89
FeatureFinderAlgorithm Base
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:64
double mz
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:87
static FeatureFinderAlgorithm * create()
UInt c
Note, this is not the charge (it is charge-1!!!)
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:88
double RT
The elution time (not the scan index)
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:91
double intensity_threshold_
The only parameter of the isotope wavelet.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:97
UInt real_RT_votes_cutoff_
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:98
double intens
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:90
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
bool check_PPMs_
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:100
Peak1D PeakType
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:65
void run() override
The working horse of this class.
std::map< UInt, BoxElement > Box
Key: RT (index), value: BoxElement.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:94
~FeatureFinderAlgorithmIsotopeWavelet() override
Destructor.
std::vector< UInt > gpu_ids_
A list of all GPU devices that can be used.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:101
Internally used data structure for the sweep line algorithm.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:86
Abstract base class for FeatureFinder algorithms.
Definition: FeatureFinderAlgorithm.h:76
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47