48 #include <OpenMS/OpenMSConfig.h> 56 class ProteinIdentification;
57 class PeptideIdentification;
96 private std::vector<Feature>,
110 using privvec::value_type;
111 using privvec::iterator;
112 using privvec::const_iterator;
113 using privvec::size_type;
114 using privvec::pointer;
115 using privvec::reference;
116 using privvec::const_reference;
117 using privvec::difference_type;
120 using privvec::begin;
124 using privvec::resize;
125 using privvec::empty;
126 using privvec::reserve;
127 using privvec::operator[];
131 using privvec::push_back;
132 using privvec::pop_back;
133 using privvec::erase;
138 typedef std::vector<FeatureType>
Base;
198 OPENMS_DLLAPI
void sortByIntensity(
bool reverse =
false);
202 OPENMS_DLLAPI
void sortByPosition();
205 OPENMS_DLLAPI
void sortByRT();
208 OPENMS_DLLAPI
void sortByMZ();
211 OPENMS_DLLAPI
void sortByOverallQuality(
bool reverse =
false);
216 OPENMS_DLLAPI
void updateRanges()
override;
219 OPENMS_DLLAPI
void swapFeaturesOnly(
FeatureMap& from);
224 OPENMS_DLLAPI
const std::vector<ProteinIdentification>& getProteinIdentifications()
const;
227 OPENMS_DLLAPI std::vector<ProteinIdentification>& getProteinIdentifications();
230 OPENMS_DLLAPI
void setProteinIdentifications(
const std::vector<ProteinIdentification>& protein_identifications);
233 OPENMS_DLLAPI
const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications()
const;
236 OPENMS_DLLAPI std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications();
239 OPENMS_DLLAPI
void setUnassignedPeptideIdentifications(
const std::vector<PeptideIdentification>& unassigned_peptide_identifications);
242 OPENMS_DLLAPI
const std::vector<DataProcessing>& getDataProcessing()
const;
245 OPENMS_DLLAPI std::vector<DataProcessing>& getDataProcessing();
248 OPENMS_DLLAPI
void setDataProcessing(
const std::vector<DataProcessing>& processing_method);
251 OPENMS_DLLAPI
void setPrimaryMSRunPath(
const StringList& s);
258 OPENMS_DLLAPI
void getPrimaryMSRunPath(
StringList& toFill)
const;
265 OPENMS_DLLAPI
void clear(
bool clear_meta_data =
true);
279 template <
typename Type>
282 Size assignments = 0;
283 assignments += ((*this).*member_function)();
284 for (Iterator iter = this->begin(); iter != this->end(); ++iter)
286 assignments += iter->applyMemberFunction(member_function);
292 template <
typename Type>
295 Size assignments = 0;
296 assignments += ((*this).*member_function)();
297 for (ConstIterator iter = this->begin(); iter != this->end(); ++iter)
299 assignments += iter->applyMemberFunction(member_function);
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Definition: FeatureMap.h:62
Base::reverse_iterator ReverseIterator
Definition: FeatureMap.h:141
An LC-MS feature.
Definition: Feature.h:70
Feature FeatureType
Definition: FeatureMap.h:136
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
AnnotationState
state of identification, use getIDState() to query it
Definition: BaseFeature.h:70
Base::const_reverse_iterator ConstReverseIterator
Definition: FeatureMap.h:142
std::vector< ProteinIdentification > protein_identifications_
protein identifications
Definition: FeatureMap.h:309
Handles the management of a position and intensity range.
Definition: RangeManager.h:47
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
RangeManager< 2 > RangeManagerType
Definition: FeatureMap.h:137
Size applyMemberFunction(Size(Type::*member_function)() const) const
The "const" variant.
Definition: FeatureMap.h:293
std::vector< Feature > privvec
Definition: FeatureMap.h:107
Manage source document information.
Definition: DocumentIdentifier.h:55
std::vector< Size > states
count each state, indexing by BaseFeature::AnnotationState
Definition: FeatureMap.h:64
A container for features.
Definition: FeatureMap.h:95
std::vector< FeatureType > Base
Definition: FeatureMap.h:138
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
A base class defining a common interface for all classes having a unique id.
Definition: UniqueIdInterface.h:51
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all features (including subordinates)...
Definition: FeatureMap.h:280
Base::iterator Iterator
Definition: FeatureMap.h:139
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
FeatureType & Reference
Definition: FeatureMap.h:143
std::vector< PeptideIdentification > unassigned_peptide_identifications_
peptide identifications not matched to a specific feature
Definition: FeatureMap.h:312
const FeatureType & ConstReference
Definition: FeatureMap.h:144
std::vector< DataProcessing > data_processing_
applied data processing
Definition: FeatureMap.h:315
Base::const_iterator ConstIterator
Definition: FeatureMap.h:140
A base class for random access containers for classes derived from UniqueIdInterface that adds functi...
Definition: UniqueIdIndexer.h:63
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46