OpenMS  2.6.0
PrecursorIonSelectionPreprocessing.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 2002-2020.
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 
36 #pragma once
37 
42 
43 #include <algorithm>
44 #include <cmath>
45 #include <set>
46 #include <fstream>
47 namespace OpenMS
48 {
49 
55  class OPENMS_DLLAPI PrecursorIonSelectionPreprocessing :
56  public DefaultParamHandler
57  {
58 public:
62 
64 
65 
66  const std::map<String, std::vector<double> > & getProtMasses() const;
67 
68 
69  const std::vector<double> & getMasses(String acc) const;
70 
71  const std::map<String, std::vector<double> > & getProteinRTMap() const;
72  const std::map<String, std::vector<double> > & getProteinPTMap() const;
73  const std::map<String, std::vector<String> > & getProteinPeptideSequenceMap() const;
74 
75 
85  void dbPreprocessing(String db_path, bool save = true);
86 
98  void dbPreprocessing(String db_path, String rt_model_path, String dt_model_path, bool save = true);
99 
100 
108  void loadPreprocessing();
109 
111  double getWeight(double mass);
112 
113  double getRT(String prot_id, Size peptide_index);
114 
115  double getPT(String prot_id, Size peptide_index);
116 
117  void setFixedModifications(StringList & modifications);
118  const std::map<char, std::vector<String> > & getFixedModifications()
119  {
120  return fixed_modifications_;
121  }
122 
123  void setGaussianParameters(double mu, double sigma);
124  double getGaussMu()
125  {
126  return mu_;
127  }
128 
129  double getGaussSigma()
130  {
131  return sigma_;
132  }
133 
134  double getRTProbability(String prot_id, Size peptide_index, Feature & feature);
135  double getRTProbability(double pred_rt, Feature & feature);
136 
137 protected:
139  void savePreprocessedDB_(String db_path, String path);
140  void savePreprocessedDBWithRT_(String db_path, String path);
142  void loadPreprocessedDB_(String path);
144  void filterTaxonomyIdentifier_(FASTAFile::FASTAEntry & entry);
145  Int getScanNumber_(double rt);
146  double getRTProbability_(double min_obs_rt, double max_obs_rt, double pred_rt);
148  void updateMembers_() override;
149 
151  std::vector<double> masses_;
153  std::set<AASequence> sequences_;
155  std::map<String, std::vector<double> > prot_masses_;
157  std::vector<double> bin_masses_;
159  std::vector<UInt> counter_;
162 
164  std::map<String, std::vector<double> > rt_prot_map_;
165  std::map<String, std::vector<double> > pt_prot_map_;
166  std::map<String, std::vector<String> > prot_peptide_seq_map_;
167  std::map<char, std::vector<String> > fixed_modifications_;
168  double sigma_;
169  double mu_;
170 
171 
172  };
173 }
174 
DefaultParamHandler.h
OpenMS::PrecursorIonSelectionPreprocessing::getFixedModifications
const std::map< char, std::vector< String > > & getFixedModifications()
Definition: PrecursorIonSelectionPreprocessing.h:118
OpenMS::PrecursorIonSelectionPreprocessing::getGaussMu
double getGaussMu()
Definition: PrecursorIonSelectionPreprocessing.h:124
OpenMS::PrecursorIonSelectionPreprocessing::sigma_
double sigma_
Definition: PrecursorIonSelectionPreprocessing.h:168
OpenMS::PrecursorIonSelectionPreprocessing::rt_prot_map_
std::map< String, std::vector< double > > rt_prot_map_
Definition: PrecursorIonSelectionPreprocessing.h:164
OpenMS::String
A more convenient string class.
Definition: String.h:59
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::PrecursorIonSelectionPreprocessing::fixed_mods_
bool fixed_mods_
Definition: PrecursorIonSelectionPreprocessing.h:163
OpenMS::FASTAFile::FASTAEntry
FASTA entry type (identifier, description and sequence)
Definition: FASTAFile.h:76
OpenMS::PrecursorIonSelectionPreprocessing::sequences_
std::set< AASequence > sequences_
the sequences of the tryptic peptides
Definition: PrecursorIonSelectionPreprocessing.h:153
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::PrecursorIonSelectionPreprocessing::mu_
double mu_
Definition: PrecursorIonSelectionPreprocessing.h:169
OpenMS::PrecursorIonSelectionPreprocessing::counter_
std::vector< UInt > counter_
counter for the bins
Definition: PrecursorIonSelectionPreprocessing.h:159
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
FASTAFile.h
int
FeatureMap.h
OpenMS::PrecursorIonSelectionPreprocessing::prot_peptide_seq_map_
std::map< String, std::vector< String > > prot_peptide_seq_map_
Definition: PrecursorIonSelectionPreprocessing.h:166
OpenMS::PrecursorIonSelectionPreprocessing::masses_
std::vector< double > masses_
all tryptic masses of the distinct peptides in the database
Definition: PrecursorIonSelectionPreprocessing.h:151
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
AASequence.h
OpenMS::PrecursorIonSelectionPreprocessing::bin_masses_
std::vector< double > bin_masses_
the masses of the bins used for preprocessing (only used if bins are not equidistant,...
Definition: PrecursorIonSelectionPreprocessing.h:157
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::PrecursorIonSelectionPreprocessing::getGaussSigma
double getGaussSigma()
Definition: PrecursorIonSelectionPreprocessing.h:129
OpenMS::PrecursorIonSelectionPreprocessing::prot_masses_
std::map< String, std::vector< double > > prot_masses_
stores masses of tryptic peptides for proteins, key is the accession number
Definition: PrecursorIonSelectionPreprocessing.h:155
OpenMS::PrecursorIonSelectionPreprocessing::pt_prot_map_
std::map< String, std::vector< double > > pt_prot_map_
Definition: PrecursorIonSelectionPreprocessing.h:165
OpenMS::PrecursorIonSelectionPreprocessing::f_max_
UInt f_max_
maximal relative frequency of a mass
Definition: PrecursorIonSelectionPreprocessing.h:161
OpenMS::PrecursorIonSelectionPreprocessing
This class implements the database preprocessing needing for precursor ion selection.
Definition: PrecursorIonSelectionPreprocessing.h:55
OpenMS::PrecursorIonSelectionPreprocessing::fixed_modifications_
std::map< char, std::vector< String > > fixed_modifications_
Definition: PrecursorIonSelectionPreprocessing.h:167