Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
SeedListGenerator.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 2002-2017.
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: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34 
35 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SEEDLISTGENERATOR_H
36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SEEDLISTGENERATOR_H
37 
45 
46 #include <vector>
47 
48 namespace OpenMS
49 {
57  class OPENMS_DLLAPI SeedListGenerator
58  {
59 public:
60 
62  typedef std::vector<DPosition<2> > SeedList;
63 
64 
67 
68 
74  void generateSeedList(const PeakMap & experiment, SeedList & seeds);
75 
76 
84  void generateSeedList(std::vector<PeptideIdentification> & peptides,
85  SeedList & seeds, bool use_peptide_mass = false);
86 
87 
96  void generateSeedLists(const ConsensusMap & consensus,
97  Map<UInt64, SeedList> & seed_lists);
98 
99 
101  void convertSeedList(const SeedList & seeds, FeatureMap & features);
102 
103 
105  void convertSeedList(const FeatureMap & features, SeedList & seeds);
106 
107  };
108 
109 }
110 
111 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SEEDLISTGENERATOR_H
std::vector< DPosition< 2 > > SeedList
List of seed positions.
Definition: SeedListGenerator.h:62
A container for features.
Definition: FeatureMap.h:94
A container for consensus elements.
Definition: ConsensusMap.h:72
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Generate seed lists for feature detection.
Definition: SeedListGenerator.h:57
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:03 using doxygen 1.8.13