OpenMS  3.0.0
QCBase.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow, Tom Waschischeck $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
40 
41 #include <map>
42 
43 namespace OpenMS
44 {
45  class MSExperiment;
46  class ConsensusMap;
47 
54  class OPENMS_DLLAPI QCBase
55  {
56  public:
60  enum class Requires
61  : UInt64 // 64 bit unsigned type for bitwise and/or operations (see below)
62  {
63  NOTHING, //< default, does not require anything
64  RAWMZML, //< mzML file is required
65  POSTFDRFEAT, //< Features with FDR-filtered pepIDs
66  PREFDRFEAT, //< Features with unfiltered pepIDs
67  CONTAMINANTS, //< Contaminant Database
68  TRAFOALIGN, //< transformationXMLs for RT-alignment
69  ID, //< idXML with protein IDs
70  SIZE_OF_REQUIRES
71  };
73  static const std::string names_of_requires[];
74 
75  enum class ToleranceUnit
76  {
77  AUTO,
78  PPM,
79  DA,
80  SIZE_OF_TOLERANCEUNIT
81  };
83  static const std::string names_of_toleranceUnit[];
84 
85 
89  class OPENMS_DLLAPI SpectraMap
90  {
91  public:
93  SpectraMap() = default;
94 
96  explicit SpectraMap(const MSExperiment& exp);
97 
99  ~SpectraMap() = default;
100 
102  void calculateMap(const MSExperiment& exp);
103 
106  UInt64 at(const String& identifier) const;
107 
109  void clear();
110 
112  bool empty() const;
113 
115  Size size() const;
116 
117  private:
118  std::map<String, UInt64> nativeid_to_index_; //< nativeID to index
119  };
120 
122 
123 
127  virtual const String& getName() const = 0;
128 
132  virtual Status requires() const = 0;
133 
134 
137  bool isRunnable(const Status& s) const;
138 
140  static bool isLabeledExperiment(const ConsensusMap& cm);
141 
143  template <typename MAP>
144  static bool hasPepID(const MAP& fmap)
145  {
146  if (!fmap.getUnassignedPeptideIdentifications().empty()) return true;
147 
148  for (const auto& features : fmap)
149  {
150  if (!features.getPeptideIdentifications().empty()) return true;
151  }
152  return false;
153  }
154  };
155 }
OpenMS::UInt64
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
Types.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::QCBase::Requires
Requires
Enum to encode a file type as a bit.
Definition: QCBase.h:60
OpenMS::QCBase::SpectraMap
Map to find a spectrum via its NativeID.
Definition: QCBase.h:89
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::QCBase
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:54
OpenMS::QCBase::SpectraMap::nativeid_to_index_
std::map< String, UInt64 > nativeid_to_index_
Definition: QCBase.h:118
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::FlagSet
Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64.
Definition: FlagSet.h:53
String.h
OpenMS::QCBase::hasPepID
static bool hasPepID(const MAP &fmap)
does the container have a PeptideIdentification in its members or as unassignedPepID ?
Definition: QCBase.h:144
FlagSet.h
OpenMS::QCBase::ToleranceUnit
ToleranceUnit
Definition: QCBase.h:75