35 #ifndef OPENMS_KERNEL_CONSENSUSMAP_H 36 #define OPENMS_KERNEL_CONSENSUSMAP_H 47 #include <OpenMS/OpenMSConfig.h> 54 class ProteinIdentification;
73 private std::vector<ConsensusFeature>,
82 typedef std::vector<ConsensusFeature>
privvec;
85 using privvec::value_type;
86 using privvec::iterator;
87 using privvec::const_iterator;
88 using privvec::size_type;
89 using privvec::pointer;
90 using privvec::reference;
91 using privvec::const_reference;
92 using privvec::difference_type;
99 using privvec::resize;
100 using privvec::empty;
101 using privvec::reserve;
102 using privvec::operator[];
106 using privvec::push_back;
116 FileDescription(
const FileDescription&);
131 typedef std::vector<ConsensusFeature>
Base;
135 typedef std::vector<ConsensusFeature>::iterator
Iterator;
175 OPENMS_DLLAPI
void clear(
bool clear_meta_data =
true);
178 OPENMS_DLLAPI
const FileDescriptions& getFileDescriptions()
const;
181 OPENMS_DLLAPI FileDescriptions& getFileDescriptions();
184 OPENMS_DLLAPI
void setFileDescriptions(
const FileDescriptions& file_description);
187 OPENMS_DLLAPI
const String& getExperimentType()
const;
190 OPENMS_DLLAPI
void setExperimentType(
const String& experiment_type);
199 OPENMS_DLLAPI
void sortByIntensity(
bool reverse =
false);
203 OPENMS_DLLAPI
void sortByRT();
206 OPENMS_DLLAPI
void sortByMZ();
209 OPENMS_DLLAPI
void sortByPosition();
212 OPENMS_DLLAPI
void sortByQuality(
bool reverse =
false);
215 OPENMS_DLLAPI
void sortBySize();
218 OPENMS_DLLAPI
void sortByMaps();
223 OPENMS_DLLAPI
void updateRanges();
229 OPENMS_DLLAPI
const std::vector<ProteinIdentification>& getProteinIdentifications()
const;
232 OPENMS_DLLAPI std::vector<ProteinIdentification>& getProteinIdentifications();
235 OPENMS_DLLAPI
void setProteinIdentifications(
const std::vector<ProteinIdentification>& protein_identifications);
238 OPENMS_DLLAPI
const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications()
const;
241 OPENMS_DLLAPI std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications();
244 OPENMS_DLLAPI
void setUnassignedPeptideIdentifications(
const std::vector<PeptideIdentification>& unassigned_peptide_identifications);
247 OPENMS_DLLAPI
const std::vector<DataProcessing>& getDataProcessing()
const;
250 OPENMS_DLLAPI std::vector<DataProcessing>& getDataProcessing();
253 OPENMS_DLLAPI
void setDataProcessing(
const std::vector<DataProcessing>& processing_method);
256 OPENMS_DLLAPI
bool operator==(
const ConsensusMap& rhs)
const;
259 OPENMS_DLLAPI
bool operator!=(
const ConsensusMap& rhs)
const;
274 template <
typename Type>
277 Size assignments = 0;
278 assignments += ((*this).*member_function)();
279 for (Iterator iter = this->begin(); iter != this->end(); ++iter)
281 assignments += ((*iter).*member_function)();
287 template <
typename Type>
290 Size assignments = 0;
291 assignments += ((*this).*member_function)();
292 for (ConstIterator iter = this->begin(); iter != this->end(); ++iter)
294 assignments += ((*iter).*member_function)();
336 #endif // OPENMS_KERNEL_CONSENSUSMAP_H
std::vector< ConsensusFeature >::iterator Iterator
Mutable iterator.
Definition: ConsensusMap.h:135
A more convenient string class.
Definition: String.h:57
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
std::vector< PeptideIdentification > unassigned_peptide_identifications_
protein identifications
Definition: ConsensusMap.h:325
UInt64 unique_id
Unique id of the file.
Definition: ConsensusMap.h:126
A container for consensus elements.
Definition: ConsensusMap.h:72
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
Log Stream Class.
Definition: LogStream.h:303
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)
A base class for random access containers for classes derived from UniqueIdInterface that adds functi...
Definition: UniqueIdIndexer.h:64
RangeManager< 2 > RangeManagerType
Definition: ConsensusMap.h:132
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
std::vector< ProteinIdentification > protein_identifications_
protein identifications
Definition: ConsensusMap.h:322
std::vector< ConsensusFeature > privvec
Definition: ConsensusMap.h:82
Handles the management of a position and intensity range.
Definition: RangeManager.h:48
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
Manage source document information.
Definition: DocumentIdentifier.h:56
Size applyMemberFunction(Size(Type::*member_function)() const) const
The "const" variant.
Definition: ConsensusMap.h:288