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ConsensusMap.h
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34 
35 #ifndef OPENMS_KERNEL_CONSENSUSMAP_H
36 #define OPENMS_KERNEL_CONSENSUSMAP_H
37 
44 
45 #include <OpenMS/CONCEPT/Types.h>
47 #include <OpenMS/OpenMSConfig.h>
48 
49 #include <map>
50 #include <vector>
51 
52 namespace OpenMS
53 {
54  class ProteinIdentification;
55  class DataProcessing;
56  namespace Logger
57  {
58  class LogStream;
59  }
60 
72  class ConsensusMap : // no OPENMS_DLLAPI here, since the class is derived from an STL class - we do not want parts of the STL lib in OpenMS.lib, since it will cause linker errors
73  private std::vector<ConsensusFeature>,
74  public MetaInfoInterface,
75  public RangeManager<2>,
76  public DocumentIdentifier,
77  public UniqueIdInterface,
78  public UniqueIdIndexer<ConsensusMap>
79  {
80 
81 public:
82  typedef std::vector<ConsensusFeature> privvec;
83 
84  // types
85  using privvec::value_type;
86  using privvec::iterator;
87  using privvec::const_iterator;
88  using privvec::size_type;
89  using privvec::pointer; // ConstRefVector
90  using privvec::reference; // ConstRefVector
91  using privvec::const_reference; // ConstRefVector
92  using privvec::difference_type; // ConstRefVector
93 
94  // functions
95  using privvec::begin;
96  using privvec::end;
97 
98  using privvec::size;
99  using privvec::resize;
100  using privvec::empty;
101  using privvec::reserve;
102  using privvec::operator[];
103  using privvec::at; // UniqueIdIndexer
104  using privvec::back; // source/ANALYSIS/DECHARGING/FeatureDeconvolution.cpp:977:
105 
106  using privvec::push_back;
107 
109  struct OPENMS_DLLAPI FileDescription :
110  public MetaInfoInterface
111  {
113  FileDescription();
114 
116  FileDescription(const FileDescription&);
117 
127  };
128 
130 
131  typedef std::vector<ConsensusFeature> Base;
133  typedef std::map<UInt64, FileDescription> FileDescriptions;
135  typedef std::vector<ConsensusFeature>::iterator Iterator;
137  typedef std::vector<ConsensusFeature>::const_iterator ConstIterator;
139  typedef std::vector<ConsensusFeature>::reverse_iterator ReverseIterator;
141  typedef std::vector<ConsensusFeature>::const_reverse_iterator ConstReverseIterator;
143 
145  OPENMS_DLLAPI ConsensusMap();
146 
148  OPENMS_DLLAPI ConsensusMap(const ConsensusMap& source);
149 
151  OPENMS_DLLAPI ~ConsensusMap();
152 
154  OPENMS_DLLAPI explicit ConsensusMap(Base::size_type n);
155 
157  OPENMS_DLLAPI ConsensusMap& operator=(const ConsensusMap& source);
158 
168  OPENMS_DLLAPI ConsensusMap& operator+=(const ConsensusMap& rhs);
169 
175  OPENMS_DLLAPI void clear(bool clear_meta_data = true);
176 
178  OPENMS_DLLAPI const FileDescriptions& getFileDescriptions() const;
179 
181  OPENMS_DLLAPI FileDescriptions& getFileDescriptions();
182 
184  OPENMS_DLLAPI void setFileDescriptions(const FileDescriptions& file_description);
185 
187  OPENMS_DLLAPI const String& getExperimentType() const;
188 
190  OPENMS_DLLAPI void setExperimentType(const String& experiment_type);
191 
199  OPENMS_DLLAPI void sortByIntensity(bool reverse = false);
201 
203  OPENMS_DLLAPI void sortByRT();
204 
206  OPENMS_DLLAPI void sortByMZ();
207 
209  OPENMS_DLLAPI void sortByPosition();
210 
212  OPENMS_DLLAPI void sortByQuality(bool reverse = false);
213 
215  OPENMS_DLLAPI void sortBySize();
216 
218  OPENMS_DLLAPI void sortByMaps();
219 
221 
222  // Docu in base class
223  OPENMS_DLLAPI void updateRanges();
224 
226  OPENMS_DLLAPI void swap(ConsensusMap& from);
227 
229  OPENMS_DLLAPI const std::vector<ProteinIdentification>& getProteinIdentifications() const;
230 
232  OPENMS_DLLAPI std::vector<ProteinIdentification>& getProteinIdentifications();
233 
235  OPENMS_DLLAPI void setProteinIdentifications(const std::vector<ProteinIdentification>& protein_identifications);
236 
238  OPENMS_DLLAPI const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications() const;
239 
241  OPENMS_DLLAPI std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications();
242 
244  OPENMS_DLLAPI void setUnassignedPeptideIdentifications(const std::vector<PeptideIdentification>& unassigned_peptide_identifications);
245 
247  OPENMS_DLLAPI const std::vector<DataProcessing>& getDataProcessing() const;
248 
250  OPENMS_DLLAPI std::vector<DataProcessing>& getDataProcessing();
251 
253  OPENMS_DLLAPI void setDataProcessing(const std::vector<DataProcessing>& processing_method);
254 
256  OPENMS_DLLAPI bool operator==(const ConsensusMap& rhs) const;
257 
259  OPENMS_DLLAPI bool operator!=(const ConsensusMap& rhs) const;
260 
274  template <typename Type>
275  Size applyMemberFunction(Size (Type::* member_function)())
276  {
277  Size assignments = 0;
278  assignments += ((*this).*member_function)();
279  for (Iterator iter = this->begin(); iter != this->end(); ++iter)
280  {
281  assignments += ((*iter).*member_function)();
282  }
283  return assignments;
284  }
285 
287  template <typename Type>
288  Size applyMemberFunction(Size (Type::* member_function)() const) const
289  {
290  Size assignments = 0;
291  assignments += ((*this).*member_function)();
292  for (ConstIterator iter = this->begin(); iter != this->end(); ++iter)
293  {
294  assignments += ((*iter).*member_function)();
295  }
296  return assignments;
297  }
298 
311  bool isMapConsistent(Logger::LogStream* stream = 0) const;
312 
313 protected:
314 
316  FileDescriptions file_description_;
317 
320 
322  std::vector<ProteinIdentification> protein_identifications_;
323 
325  std::vector<PeptideIdentification> unassigned_peptide_identifications_;
326 
328  std::vector<DataProcessing> data_processing_;
329  };
330 
332  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ConsensusMap& cons_map);
333 
334 } // namespace OpenMS
335 
336 #endif // OPENMS_KERNEL_CONSENSUSMAP_H
void setDataProcessing(const std::vector< DataProcessing > &processing_method)
sets the description of the applied data processing
std::vector< ConsensusFeature >::iterator Iterator
Mutable iterator.
Definition: ConsensusMap.h:135
void sortByMZ()
Sorts the peaks to m/z position.
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
A more convenient string class.
Definition: String.h:57
void clear(bool clear_meta_data=true)
Clears all data and meta data.
String label
Label e.g. 'heavy' and 'light' for ICAT, or 'sample1' and 'sample2' for label-free quantitation...
Definition: ConsensusMap.h:121
std::vector< ConsensusFeature >::const_reverse_iterator ConstReverseIterator
Non-mutable reverse iterator.
Definition: ConsensusMap.h:141
Source file description for input files.
Definition: ConsensusMap.h:109
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
std::vector< PeptideIdentification > unassigned_peptide_identifications_
protein identifications
Definition: ConsensusMap.h:325
const FileDescriptions & getFileDescriptions() const
Non-mutable access to the file descriptions.
UInt64 unique_id
Unique id of the file.
Definition: ConsensusMap.h:126
A container for consensus elements.
Definition: ConsensusMap.h:72
void sortByQuality(bool reverse=false)
Sorts the peaks according to ascending quality.
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all consensus features. The returned values are accumulated.
Definition: ConsensusMap.h:275
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::vector< DataProcessing > data_processing_
applied data processing
Definition: ConsensusMap.h:328
void setExperimentType(const String &experiment_type)
Mutable access to the experiment type.
ConsensusMap()
Default constructor.
Log Stream Class.
Definition: LogStream.h:303
~ConsensusMap()
Destructor.
const String & getExperimentType() const
Non-mutable access to the experiment type.
FileDescriptions file_description_
Map from index to file description.
Definition: ConsensusMap.h:316
std::vector< ConsensusFeature >::reverse_iterator ReverseIterator
Mutable reverse iterator.
Definition: ConsensusMap.h:139
String experiment_type_
type of experiment (label-free, itraq, ...); see xsd schema
Definition: ConsensusMap.h:319
std::vector< ConsensusFeature > Base
Definition: ConsensusMap.h:131
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
void sortByMaps()
Sorts with respect to the sets of maps covered by the consensus features (lexicographically).
A base class for random access containers for classes derived from UniqueIdInterface that adds functi...
Definition: UniqueIdIndexer.h:64
void setFileDescriptions(const FileDescriptions &file_description)
Mutable access to the file descriptions.
RangeManager< 2 > RangeManagerType
Definition: ConsensusMap.h:132
void setUnassignedPeptideIdentifications(const std::vector< PeptideIdentification > &unassigned_peptide_identifications)
sets the unassigned peptide identifications
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:71
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:56
std::map< UInt64, FileDescription > FileDescriptions
Definition: ConsensusMap.h:133
A base class defining a common interface for all classes having a unique id.
Definition: UniqueIdInterface.h:52
const std::vector< DataProcessing > & getDataProcessing() const
returns a const reference to the description of the applied data processing
std::vector< ProteinIdentification > protein_identifications_
protein identifications
Definition: ConsensusMap.h:322
ConsensusMap & operator=(const ConsensusMap &source)
Assignment operator.
void sortBySize()
Sorts with respect to the size (number of elements)
std::vector< ConsensusFeature > privvec
Definition: ConsensusMap.h:82
void swap(ConsensusMap &from)
Swaps the content of this map with the content of from.
bool isMapConsistent(Logger::LogStream *stream=0) const
checks if the given maps are unique and all FeatureHandles actually refer to a registered map ...
bool operator==(const ConsensusMap &rhs) const
Equality operator.
bool operator!=(const ConsensusMap &rhs) const
Equality operator.
void sortByPosition()
Lexicographically sorts the peaks by their position (First RT then m/z).
Handles the management of a position and intensity range.
Definition: RangeManager.h:48
void updateRanges()
Updates minimum and maximum position/intensity.
std::vector< ConsensusFeature >::const_iterator ConstIterator
Non-mutable iterator.
Definition: ConsensusMap.h:137
String filename
File name of the file.
Definition: ConsensusMap.h:119
Size size
Number of elements (features, peaks, ...). This is e.g. used to check for correct element indices whe...
Definition: ConsensusMap.h:124
void setProteinIdentifications(const std::vector< ProteinIdentification > &protein_identifications)
sets the protein identifications
void sortByRT()
Sorts the peaks to RT position.
ConsensusMap & operator+=(const ConsensusMap &rhs)
Add one consensus map to another.
Manage source document information.
Definition: DocumentIdentifier.h:56
void sortByIntensity(bool reverse=false)
Sorts the peaks according to ascending intensity.
Size applyMemberFunction(Size(Type::*member_function)() const) const
The "const" variant.
Definition: ConsensusMap.h:288

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:44 using doxygen 1.8.9.1