OpenMS  3.0.0
Observation.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: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
40 
41 #include <boost/multi_index_container.hpp>
42 #include <boost/multi_index/ordered_index.hpp>
43 #include <boost/multi_index/composite_key.hpp>
44 #include <boost/multi_index/member.hpp>
45 
46 namespace OpenMS
47 {
48  namespace IdentificationDataInternal
49  {
54  {
57 
60 
61  double rt, mz; //< Position
62 
64  explicit Observation(
65  const String& data_id,
66  const InputFileRef& input_file,
67  double rt = std::numeric_limits<double>::quiet_NaN(),
68  double mz = std::numeric_limits<double>::quiet_NaN()):
70  {
71  }
72 
74  Observation& merge(const Observation& other)
75  {
76  // merge meta info - existing entries may be overwritten:
77  addMetaValues(other);
78  rt = other.rt;
79  mz = other.mz;
80  return *this;
81  }
82  };
83 
84  // combination of input file and data ID must be unique:
85  typedef boost::multi_index_container<
86  Observation,
87  boost::multi_index::indexed_by<
88  boost::multi_index::ordered_unique<
89  boost::multi_index::composite_key<
90  Observation,
91  boost::multi_index::member<Observation, InputFileRef,
93  boost::multi_index::member<Observation, String,
97  }
98 }
OpenMS::IdentificationDataInternal::Observation::Observation
Observation(const String &data_id, const InputFileRef &input_file, double rt=std::numeric_limits< double >::quiet_NaN(), double mz=std::numeric_limits< double >::quiet_NaN())
Constructor.
Definition: Observation.h:64
MetaData.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IdentificationDataInternal::ObservationRef
IteratorWrapper< Observations::iterator > ObservationRef
Definition: Observation.h:96
OpenMS::IdentificationDataInternal::Observation::mz
double mz
Definition: Observation.h:61
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::IdentificationDataInternal::Observation::rt
double rt
Definition: Observation.h:61
OpenMS::IdentificationDataInternal::Observation
Representation of an observation, e.g. a spectrum or feature, in an input data file.
Definition: Observation.h:53
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::IdentificationDataInternal::IteratorWrapper< InputFiles::iterator >
OpenMS::MetaInfoInterface::addMetaValues
void addMetaValues(const MetaInfoInterface &from)
function to copy all meta values from one object to this one
OpenMS::IdentificationDataInternal::Observations
boost::multi_index_container< Observation, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::composite_key< Observation, boost::multi_index::member< Observation, InputFileRef, &Observation::input_file >, boost::multi_index::member< Observation, String, &Observation::data_id > > > > > Observations
Definition: Observation.h:95
OpenMS::IdentificationDataInternal::InputFileRef
IteratorWrapper< InputFiles::iterator > InputFileRef
Definition: include/OpenMS/METADATA/ID/InputFile.h:95
MetaInfoInterface.h
OpenMS::IdentificationDataInternal::Observation::data_id
String data_id
Spectrum or feature ID (from the file referenced by @t input_file)
Definition: Observation.h:56
OpenMS::IdentificationDataInternal::Observation::merge
Observation & merge(const Observation &other)
Merge in data from another object.
Definition: Observation.h:74
InputFile.h
OpenMS::IdentificationDataInternal::Observation::input_file
InputFileRef input_file
Reference to the input file.
Definition: Observation.h:59