29 #include <OpenMS/OpenMSConfig.h>
35 class ProteinIdentification;
36 class PeptideIdentification;
156 void sortByPosition();
165 void sortByOverallQuality(
bool reverse = false);
170 void updateRanges() override;
222 void clear(
bool clear_meta_data = true);
236 template <typename Type>
237 Size applyMemberFunction(
Size (Type::* member_function)())
239 Size assignments = 0;
240 assignments += ((*this).*member_function)();
241 for (
Iterator iter = this->begin(); iter != this->end(); ++iter)
243 assignments += iter->applyMemberFunction(member_function);
249 template <
typename Type>
252 Size assignments = 0;
253 assignments += ((*this).*member_function)();
254 for (
ConstIterator iter = this->begin(); iter != this->end(); ++iter)
256 assignments += iter->applyMemberFunction(member_function);
#define EXPOSED_VECTOR_INTERFACE(InnerElement)
Macro to expose common dependent types, such as iterator in the derived class.
Definition: ExposedVector.h:26
AnnotationState
state of identification, use getAnnotationState() to query it
Definition: BaseFeature.h:47
Description of the applied preprocessing steps.
Definition: DataProcessing.h:27
Manage source document information.
Definition: DocumentIdentifier.h:30
Definition: ExposedVector.h:62
typename VecMember::iterator iterator
Definition: ExposedVector.h:68
typename VecMember::const_iterator const_iterator
Definition: ExposedVector.h:69
typename VecMember::reverse_iterator reverse_iterator
Definition: ExposedVector.h:70
typename VecMember::const_reverse_iterator const_reverse_iterator
Definition: ExposedVector.h:71
A container for features.
Definition: FeatureMap.h:82
const_reverse_iterator ConstReverseIterator
Definition: FeatureMap.h:92
reverse_iterator ReverseIterator
Definition: FeatureMap.h:91
std::vector< DataProcessing > data_processing_
applied data processing
Definition: FeatureMap.h:289
IdentificationData & getIdentificationData()
Mutable access to the contained identification data.
const_iterator ConstIterator
Definition: FeatureMap.h:90
IdentificationData id_data_
general identification results (peptides/proteins, RNA, compounds)
Definition: FeatureMap.h:292
AnnotationStatistics getAnnotationStatistics() const
const IdentificationData & getIdentificationData() const
Immutable access to the contained identification data.
std::vector< ProteinIdentification > protein_identifications_
protein identifications
Definition: FeatureMap.h:283
std::set< IdentificationData::ObservationMatchRef > getUnassignedIDMatches() const
Return observation matches (e.g. PSMs) from the identification data that are not assigned to any feat...
PeptideIdentificationList unassigned_peptide_identifications_
peptide identifications not matched to a specific feature
Definition: FeatureMap.h:286
Size applyMemberFunction(Size(Type::*member_function)() const) const
The "const" variant.
Definition: FeatureMap.h:250
An LC-MS feature.
Definition: Feature.h:46
Definition: IdentificationData.h:87
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:49
Utilities for Feature and ConsensusMap.
Definition: MapUtilities.h:25
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.h:66
Representation of a protein identification run.
Definition: ProteinIdentification.h:51
Definition: RangeManager.h:889
Handles the management of a multidimensional range, e.g. RangeMZ and RangeIntensity for spectra.
Definition: RangeManager.h:568
A base class for containers with elements derived from UniqueIdInterface. This adds functionality to ...
Definition: UniqueIdIndexer.h:41
A base class defining a common interface for all classes having a unique id.
Definition: UniqueIdInterface.h:25
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
static String & reverse(String &this_s)
Definition: StringUtilsSimple.h:330
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
Definition: FeatureMap.h:42
AnnotationStatistics(const AnnotationStatistics &rhs)
std::vector< Size > states
count each state, indexing by BaseFeature::AnnotationState
Definition: FeatureMap.h:43
AnnotationStatistics & operator+=(BaseFeature::AnnotationState state)
AnnotationStatistics & operator=(const AnnotationStatistics &rhs)
bool operator==(const AnnotationStatistics &rhs) const
Definition: RangeManager.h:420
Definition: RangeManager.h:358
Definition: RangeManager.h:295