OpenMS  3.0.0
ConsensusMap.h
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31 // $Maintainer: Timo Sachsenberg $
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34 
35 #pragma once
36 
42 
45 
46 #include <OpenMS/CONCEPT/Types.h>
50 #include <OpenMS/OpenMSConfig.h>
51 
52 #include <map>
53 #include <vector>
54 #include <iosfwd>
55 
56 namespace OpenMS
57 {
58  class PeptideIdentification;
59  class PeptideHit;
60  class ProteinIdentification;
61  class DataProcessing;
62  namespace Logger
63  {
64  class LogStream;
65  }
66 
82  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
83  private std::vector<ConsensusFeature>,
84  public MetaInfoInterface,
85  public RangeManagerContainer<RangeRT, RangeMZ, RangeIntensity>,
86  public DocumentIdentifier,
87  public UniqueIdInterface,
88  public UniqueIdIndexer<ConsensusMap>,
89  public MapUtilities<ConsensusMap>
90  {
91 
92 public:
93  typedef std::vector<ConsensusFeature> privvec;
94 
95  // types
96  using privvec::value_type;
97  using privvec::iterator;
98  using privvec::const_iterator;
99  using privvec::size_type;
100  using privvec::pointer; // ConstRefVector
101  using privvec::reference; // ConstRefVector
102  using privvec::const_reference; // ConstRefVector
103  using privvec::difference_type; // ConstRefVector
104 
105  // functions
106  using privvec::begin;
107  using privvec::end;
108  using privvec::cbegin;
109  using privvec::cend;
110 
111  using privvec::size;
112  using privvec::resize;
113  using privvec::empty;
114  using privvec::reserve;
115  using privvec::operator[];
116  using privvec::at;
117  using privvec::back;
118  using privvec::push_back;
119  using privvec::emplace_back;
120  using privvec::erase;
121 
122  enum class SplitMeta
123  {
124  DISCARD,
125  COPY_ALL,
126  COPY_FIRST
127  };
128 
130  struct OPENMS_DLLAPI ColumnHeader :
131  public MetaInfoInterface
132  {
134  ColumnHeader() = default;
135 
137  ColumnHeader(const ColumnHeader&) = default;
138 
140  ColumnHeader& operator=(const ColumnHeader&) = default;
141 
144 
147 
150  Size size = 0;
151 
154 
155  unsigned getLabelAsUInt(const String& experiment_type) const;
156  };
157 
159 
161  typedef std::vector<ConsensusFeature> Base;
164  typedef std::map<UInt64, ColumnHeader> ColumnHeaders;
166  typedef std::vector<ConsensusFeature>::iterator Iterator;
168  typedef std::vector<ConsensusFeature>::const_iterator ConstIterator;
170  typedef std::vector<ConsensusFeature>::reverse_iterator ReverseIterator;
172  typedef std::vector<ConsensusFeature>::const_reverse_iterator ConstReverseIterator;
174 
176  OPENMS_DLLAPI ConsensusMap();
177 
179  OPENMS_DLLAPI ConsensusMap(const ConsensusMap& source);
180 
182  OPENMS_DLLAPI ~ConsensusMap() override;
183 
185  OPENMS_DLLAPI explicit ConsensusMap(Base::size_type n);
186 
188  OPENMS_DLLAPI ConsensusMap& operator=(const ConsensusMap& source);
189 
199  OPENMS_DLLAPI ConsensusMap& appendRows(const ConsensusMap& rhs);
200 
208  OPENMS_DLLAPI ConsensusMap& appendColumns(const ConsensusMap& rhs);
209 
210 
216  OPENMS_DLLAPI void clear(bool clear_meta_data = true);
217 
219  OPENMS_DLLAPI const ColumnHeaders& getColumnHeaders() const;
220 
222  OPENMS_DLLAPI ColumnHeaders& getColumnHeaders();
223 
225  OPENMS_DLLAPI void setColumnHeaders(const ColumnHeaders& column_description);
226 
228  OPENMS_DLLAPI const String& getExperimentType() const;
229 
231  OPENMS_DLLAPI void setExperimentType(const String& experiment_type);
232 
240  OPENMS_DLLAPI void sortByIntensity(bool reverse = false);
242 
244  OPENMS_DLLAPI void sortByRT();
245 
247  OPENMS_DLLAPI void sortByMZ();
248 
250  OPENMS_DLLAPI void sortByPosition();
251 
253  OPENMS_DLLAPI void sortByQuality(bool reverse = false);
254 
256  OPENMS_DLLAPI void sortBySize();
257 
259  OPENMS_DLLAPI void sortByMaps();
260 
262  OPENMS_DLLAPI void sortPeptideIdentificationsByMapIndex();
264 
265  // Docu in base class
266  OPENMS_DLLAPI void updateRanges() override;
267 
269  OPENMS_DLLAPI void swap(ConsensusMap& from);
270 
272  OPENMS_DLLAPI const std::vector<ProteinIdentification>& getProteinIdentifications() const;
273 
275  OPENMS_DLLAPI std::vector<ProteinIdentification>& getProteinIdentifications();
276 
278  OPENMS_DLLAPI void setProteinIdentifications(const std::vector<ProteinIdentification>& protein_identifications);
279 
281  OPENMS_DLLAPI void setProteinIdentifications(std::vector<ProteinIdentification>&& protein_identifications);
282 
284  OPENMS_DLLAPI const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications() const;
285 
287  OPENMS_DLLAPI std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications();
288 
290  OPENMS_DLLAPI void setUnassignedPeptideIdentifications(const std::vector<PeptideIdentification>& unassigned_peptide_identifications);
291 
293  OPENMS_DLLAPI const std::vector<DataProcessing>& getDataProcessing() const;
294 
296  OPENMS_DLLAPI std::vector<DataProcessing>& getDataProcessing();
297 
299  OPENMS_DLLAPI void setDataProcessing(const std::vector<DataProcessing>& processing_method);
300 
302  OPENMS_DLLAPI void setPrimaryMSRunPath(const StringList& s);
303 
308  OPENMS_DLLAPI void setPrimaryMSRunPath(const StringList& s, MSExperiment & e);
309 
311  OPENMS_DLLAPI void getPrimaryMSRunPath(StringList& toFill) const;
312 
314  OPENMS_DLLAPI bool operator==(const ConsensusMap& rhs) const;
315 
317  OPENMS_DLLAPI bool operator!=(const ConsensusMap& rhs) const;
318 
332  template <typename Type>
333  Size applyMemberFunction(Size (Type::* member_function)())
334  {
335  Size assignments = 0;
336  assignments += ((*this).*member_function)();
337  for (Iterator iter = this->begin(); iter != this->end(); ++iter)
338  {
339  assignments += ((*iter).*member_function)();
340  }
341  return assignments;
342  }
343 
345  template <typename Type>
346  Size applyMemberFunction(Size (Type::* member_function)() const) const
347  {
348  Size assignments = 0;
349  assignments += ((*this).*member_function)();
350  for (ConstIterator iter = this->begin(); iter != this->end(); ++iter)
351  {
352  assignments += ((*iter).*member_function)();
353  }
354  return assignments;
355  }
356 
369  OPENMS_DLLAPI bool isMapConsistent(Logger::LogStream* stream = nullptr) const;
370 
384  OPENMS_DLLAPI std::vector<FeatureMap> split(SplitMeta mode = SplitMeta::DISCARD) const;
385 
386 protected:
387 
390 
392  String experiment_type_ = "label-free";
393 
395  std::vector<ProteinIdentification> protein_identifications_;
396 
398  std::vector<PeptideIdentification> unassigned_peptide_identifications_;
399 
401  std::vector<DataProcessing> data_processing_;
402 
403  };
404 
406  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ConsensusMap& cons_map);
407 
408 } // namespace OpenMS
409 
LogStream.h
OpenMS::ConsensusMap::operator=
ConsensusMap & operator=(const ConsensusMap &source)
Assignment operator.
OpenMS::ConsensusMap::sortByQuality
void sortByQuality(bool reverse=false)
Sorts the peaks according to ascending quality.
UniqueIdInterface.h
OpenMS::ConsensusMap::ColumnHeader
Description of the columns in a consensus map.
Definition: ConsensusMap.h:130
OpenMS::ConsensusMap::applyMemberFunction
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all consensus features....
Definition: ConsensusMap.h:333
OpenMS::ConsensusMap::ColumnHeader::filename
String filename
File name of the mzML file.
Definition: ConsensusMap.h:143
OpenMS::ConsensusMap::protein_identifications_
std::vector< ProteinIdentification > protein_identifications_
protein identifications
Definition: ConsensusMap.h:395
OpenMS::UInt64
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
OpenMS::ConsensusMap::sortBySize
void sortBySize()
Sorts with respect to the size (number of elements)
Types.h
OpenMS::ConsensusMap::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position (First RT then m/z).
OpenMS::ConsensusMap::updateRanges
void updateRanges() override
DocumentIdentifier.h
OpenMS::StringUtils::reverse
static String & reverse(String &this_s)
Definition: StringUtilsSimple.h:350
OpenMS::ConsensusMap::SplitMeta
SplitMeta
Definition: ConsensusMap.h:122
OpenMS::ConsensusMap::split
std::vector< FeatureMap > split(SplitMeta mode=SplitMeta::DISCARD) const
splits ConsensusMap into its original FeatureMaps
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::UniqueIdInterface
A base class defining a common interface for all classes having a unique id.
Definition: UniqueIdInterface.h:50
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ConsensusMap::getExperimentType
const String & getExperimentType() const
Non-mutable access to the experiment type.
OpenMS::ConsensusMap::getPrimaryMSRunPath
void getPrimaryMSRunPath(StringList &toFill) const
returns the MS run path (stored in ColumnHeaders)
OpenMS::ConsensusMap::sortByMaps
void sortByMaps()
Sorts with respect to the sets of maps covered by the consensus features (lexicographically).
MapUtilities.h
OpenMS::ConsensusMap::sortByIntensity
void sortByIntensity(bool reverse=false)
Sorts the peaks according to ascending intensity.
ConsensusFeature.h
OpenMS::ConsensusMap::sortPeptideIdentificationsByMapIndex
void sortPeptideIdentificationsByMapIndex()
Sorts PeptideIdentifications of consensus features with respect to their map index.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::RangeManager
Handles the management of a multidimensional range, e.g. RangeMZ and RangeIntensity for spectra.
Definition: RangeManager.h:588
OpenMS::ConsensusMap::operator!=
bool operator!=(const ConsensusMap &rhs) const
Equality operator.
OpenMS::ConsensusMap::applyMemberFunction
Size applyMemberFunction(Size(Type::*member_function)() const) const
The "const" variant.
Definition: ConsensusMap.h:346
OpenMS::ConsensusMap::appendColumns
ConsensusMap & appendColumns(const ConsensusMap &rhs)
Add consensus map entries as new columns.
OpenMS::ConsensusMap::swap
void swap(ConsensusMap &from)
Swaps the content of this map with the content of from.
OpenMS::ConsensusMap::unassigned_peptide_identifications_
std::vector< PeptideIdentification > unassigned_peptide_identifications_
unassigned peptide identifications (without feature)
Definition: ConsensusMap.h:398
OpenMS::UniqueIdIndexer
A base class for random access containers for classes derived from UniqueIdInterface that adds functi...
Definition: UniqueIdIndexer.h:63
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::DocumentIdentifier
Manage source document information.
Definition: DocumentIdentifier.h:55
OpenMS::ConsensusMap::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
OpenMS::ConsensusMap::setColumnHeaders
void setColumnHeaders(const ColumnHeaders &column_description)
Mutable access to the file descriptions.
OpenMS::ConsensusMap::FeatureType
ConsensusFeature FeatureType
Definition: ConsensusMap.h:160
UniqueIdIndexer.h
OpenMS::ConsensusMap::privvec
std::vector< ConsensusFeature > privvec
Definition: ConsensusMap.h:93
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::ConsensusMap::ConstIterator
std::vector< ConsensusFeature >::const_iterator ConstIterator
Non-mutable iterator.
Definition: ConsensusMap.h:168
OpenMS::ConsensusMap::appendRows
ConsensusMap & appendRows(const ConsensusMap &rhs)
Add consensus map entries as new rows.
OpenMS::ConsensusMap::RangeManagerType
RangeManager< RangeRT, RangeMZ, RangeIntensity > RangeManagerType
Definition: ConsensusMap.h:163
OpenMS::ConsensusMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::ConsensusMap::ColumnHeader::label
String label
Label e.g. 'heavy' and 'light' for ICAT, or 'sample1' and 'sample2' for label-free quantitation.
Definition: ConsensusMap.h:146
OpenMS::ConsensusMap::setProteinIdentifications
void setProteinIdentifications(const std::vector< ProteinIdentification > &protein_identifications)
sets the protein identifications
OpenMS::UniqueIdInterface::INVALID
Definition: UniqueIdInterface.h:60
RangeManager.h
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::Logger::LogStream
Log Stream Class.
Definition: LogStream.h:311
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::ConsensusMap::SplitMeta::COPY_ALL
copy all meta values to all feature maps
OpenMS::RangeManagerContainer
Definition: RangeManager.h:919
OpenMS::ConsensusMap::sortByRT
void sortByRT()
Sorts the peaks to RT position.
OpenMS::ConsensusMap::~ConsensusMap
~ConsensusMap() override
Destructor.
MSExperiment.h
OpenMS::ConsensusMap::getColumnHeaders
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
OpenMS::ConsensusMap::ConsensusMap
ConsensusMap()
Default constructor.
OpenMS::ConsensusMap::getDataProcessing
const std::vector< DataProcessing > & getDataProcessing() const
returns a const reference to the description of the applied data processing
OpenMS::ConsensusMap::clear
void clear(bool clear_meta_data=true)
Clears all data and meta data.
OpenMS::ConsensusMap::Iterator
std::vector< ConsensusFeature >::iterator Iterator
Mutable iterator.
Definition: ConsensusMap.h:166
OpenMS::ConsensusMap::setDataProcessing
void setDataProcessing(const std::vector< DataProcessing > &processing_method)
sets the description of the applied data processing
MetaInfoInterface.h
OpenMS::ConsensusMap::SplitMeta::COPY_FIRST
copy all meta values to first feature map
OpenMS::ConsensusMap::sortByMZ
void sortByMZ()
Sorts the peaks to m/z position.
String.h
OpenMS::ConsensusMap::ReverseIterator
std::vector< ConsensusFeature >::reverse_iterator ReverseIterator
Mutable reverse iterator.
Definition: ConsensusMap.h:170
OpenMS::ConsensusMap::RangeManagerContainerType
RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity > RangeManagerContainerType
Definition: ConsensusMap.h:162
OpenMS::ConsensusMap::ConstReverseIterator
std::vector< ConsensusFeature >::const_reverse_iterator ConstReverseIterator
Non-mutable reverse iterator.
Definition: ConsensusMap.h:172
OpenMS::MapUtilities
Utilities for Feature and ConsensusMap.
Definition: MapUtilities.h:49
OpenMS::ConsensusMap::SplitMeta::DISCARD
do not copy any meta values
OpenMS::ConsensusMap::experiment_type_
String experiment_type_
type of experiment (label-free, labeled_MS1, labeled_MS2)
Definition: ConsensusMap.h:392
OpenMS::ConsensusMap::Base
std::vector< ConsensusFeature > Base
Definition: ConsensusMap.h:161
OpenMS::ConsensusMap::isMapConsistent
bool isMapConsistent(Logger::LogStream *stream=nullptr) const
checks if the given maps are unique and all FeatureHandles actually refer to a registered map
OpenMS::ConsensusMap::operator==
bool operator==(const ConsensusMap &rhs) const
Equality operator.
OpenMS::ConsensusMap::data_processing_
std::vector< DataProcessing > data_processing_
applied data processing
Definition: ConsensusMap.h:401
OpenMS::ConsensusMap::setExperimentType
void setExperimentType(const String &experiment_type)
Mutable access to the experiment type.
OpenMS::ConsensusMap::setPrimaryMSRunPath
void setPrimaryMSRunPath(const StringList &s)
set the file paths to the primary MS run (stored in ColumnHeaders)
OpenMS::ConsensusMap::column_description_
ColumnHeaders column_description_
Map from index to file description.
Definition: ConsensusMap.h:389
OpenMS::ConsensusMap::ColumnHeaders
std::map< UInt64, ColumnHeader > ColumnHeaders
Definition: ConsensusMap.h:164
OpenMS::ConsensusMap::setUnassignedPeptideIdentifications
void setUnassignedPeptideIdentifications(const std::vector< PeptideIdentification > &unassigned_peptide_identifications)
sets the unassigned peptide identifications