46 #include <OpenMS/OpenMSConfig.h> 54 class ProteinIdentification;
55 class PeptideIdentification;
94 private std::vector<Feature>,
108 using privvec::value_type;
109 using privvec::iterator;
110 using privvec::const_iterator;
111 using privvec::size_type;
112 using privvec::pointer;
113 using privvec::reference;
114 using privvec::const_reference;
115 using privvec::difference_type;
118 using privvec::begin;
122 using privvec::resize;
123 using privvec::empty;
124 using privvec::reserve;
125 using privvec::operator[];
129 using privvec::push_back;
130 using privvec::pop_back;
131 using privvec::erase;
136 typedef std::vector<FeatureType>
Base;
196 OPENMS_DLLAPI
void sortByIntensity(
bool reverse =
false);
200 OPENMS_DLLAPI
void sortByPosition();
203 OPENMS_DLLAPI
void sortByRT();
206 OPENMS_DLLAPI
void sortByMZ();
209 OPENMS_DLLAPI
void sortByOverallQuality(
bool reverse =
false);
214 OPENMS_DLLAPI
void updateRanges()
override;
217 OPENMS_DLLAPI
void swapFeaturesOnly(
FeatureMap& from);
222 OPENMS_DLLAPI
const std::vector<ProteinIdentification>& getProteinIdentifications()
const;
225 OPENMS_DLLAPI std::vector<ProteinIdentification>& getProteinIdentifications();
228 OPENMS_DLLAPI
void setProteinIdentifications(
const std::vector<ProteinIdentification>& protein_identifications);
231 OPENMS_DLLAPI
const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications()
const;
234 OPENMS_DLLAPI std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications();
237 OPENMS_DLLAPI
void setUnassignedPeptideIdentifications(
const std::vector<PeptideIdentification>& unassigned_peptide_identifications);
240 OPENMS_DLLAPI
const std::vector<DataProcessing>& getDataProcessing()
const;
243 OPENMS_DLLAPI std::vector<DataProcessing>& getDataProcessing();
246 OPENMS_DLLAPI
void setDataProcessing(
const std::vector<DataProcessing>& processing_method);
249 OPENMS_DLLAPI
void setPrimaryMSRunPath(
const StringList& s);
252 OPENMS_DLLAPI
void getPrimaryMSRunPath(
StringList& toFill)
const;
259 OPENMS_DLLAPI
void clear(
bool clear_meta_data =
true);
273 template <
typename Type>
276 Size assignments = 0;
277 assignments += ((*this).*member_function)();
278 for (Iterator iter = this->begin(); iter != this->end(); ++iter)
280 assignments += iter->applyMemberFunction(member_function);
286 template <
typename Type>
289 Size assignments = 0;
290 assignments += ((*this).*member_function)();
291 for (ConstIterator iter = this->begin(); iter != this->end(); ++iter)
293 assignments += iter->applyMemberFunction(member_function);
Base::const_iterator ConstIterator
Definition: FeatureMap.h:138
std::vector< Size > states
count each state, indexing by BaseFeature::AnnotationState
Definition: FeatureMap.h:62
Size applyMemberFunction(Size(Type::*member_function)() const) const
The "const" variant.
Definition: FeatureMap.h:287
A container for features.
Definition: FeatureMap.h:93
Base::reverse_iterator ReverseIterator
Definition: FeatureMap.h:139
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
FeatureType & Reference
Definition: FeatureMap.h:141
Feature FeatureType
Definition: FeatureMap.h:134
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all features (including subordinates)...
Definition: FeatureMap.h:274
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Base::const_reverse_iterator ConstReverseIterator
Definition: FeatureMap.h:140
const FeatureType & ConstReference
Definition: FeatureMap.h:142
RangeManager< 2 > RangeManagerType
Definition: FeatureMap.h:135
std::vector< ProteinIdentification > protein_identifications_
protein identifications
Definition: FeatureMap.h:303
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:63
Base::iterator Iterator
Definition: FeatureMap.h:137
An LC-MS feature.
Definition: Feature.h:70
std::vector< Feature > privvec
Definition: FeatureMap.h:105
std::vector< PeptideIdentification > unassigned_peptide_identifications_
peptide identifications not matched to a specific feature
Definition: FeatureMap.h:306
A base class defining a common interface for all classes having a unique id.
Definition: UniqueIdInterface.h:51
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
std::vector< FeatureType > Base
Definition: FeatureMap.h:136
std::vector< DataProcessing > data_processing_
applied data processing
Definition: FeatureMap.h:309
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
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:69
Definition: FeatureMap.h:60
Handles the management of a position and intensity range.
Definition: RangeManager.h:47
Manage source document information.
Definition: DocumentIdentifier.h:55