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;
248 OPENMS_DLLAPI
void setDataProcessing(
const std::vector<DataProcessing>& processing_method);
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);
An LC-MS feature.
Definition: Feature.h:70
Definition: FeatureMap.h:62
Size applyMemberFunction(Size(Type::*member_function)() const) const
The "const" variant.
Definition: FeatureMap.h:293
void clear(bool clear_meta_data=true)
Clears all data and meta data.
void sortByRT()
Sort features by RT position.
std::vector< FeatureType > Base
Definition: FeatureMap.h:138
Handles the management of a position and intensity range.
Definition: RangeManager.h:47
void setDataProcessing(const std::vector< DataProcessing > &processing_method)
sets the description of the applied data processing
void sortByMZ()
Sort features by m/z position.
FeatureMap()
Default constructor.
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
const FeatureType & ConstReference
Definition: FeatureMap.h:144
std::vector< DataProcessing > data_processing_
applied data processing
Definition: FeatureMap.h:315
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
A container for features.
Definition: FeatureMap.h:95
const std::vector< DataProcessing > & getDataProcessing() const
returns a const reference to the description of the applied data processing
void updateRanges() override
Updates minimum and maximum position/intensity.
FeatureMap operator+(const FeatureMap &rhs) const
Joins two feature maps.
~FeatureMap() override
Destructor.
Manage source document information.
Definition: DocumentIdentifier.h:55
FeatureType & Reference
Definition: FeatureMap.h:143
std::vector< PeptideIdentification > unassigned_peptide_identifications_
peptide identifications not matched to a specific feature
Definition: FeatureMap.h:312
Base::const_iterator ConstIterator
Definition: FeatureMap.h:140
AnnotationStatistics getAnnotationStatistics() const
void setUnassignedPeptideIdentifications(const std::vector< PeptideIdentification > &unassigned_peptide_identifications)
sets the unassigned peptide identifications
A base class defining a common interface for all classes having a unique id.
Definition: UniqueIdInterface.h:51
void setProteinIdentifications(const std::vector< ProteinIdentification > &protein_identifications)
sets the protein identifications
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void sortByIntensity(bool reverse=false)
Sorts the peaks according to ascending intensity.
void swap(FeatureMap &from)
Base::reverse_iterator ReverseIterator
Definition: FeatureMap.h:141
Feature FeatureType
Definition: FeatureMap.h:136
bool operator==(const FeatureMap &rhs) const
Equality operator.
A base class for random access containers for classes derived from UniqueIdInterface that adds functi...
Definition: UniqueIdIndexer.h:63
bool operator!=(const FeatureMap &rhs) const
Equality operator.
std::vector< Size > states
count each state, indexing by BaseFeature::AnnotationState
Definition: FeatureMap.h:64
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
FeatureMap & operator=(const FeatureMap &rhs)
Assignment operator.
void sortByOverallQuality(bool reverse=false)
Sort features by ascending overall quality.
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
RangeManager< 2 > RangeManagerType
Definition: FeatureMap.h:137
void getPrimaryMSRunPath(StringList &toFill) const
get the file path to the first MS run
std::vector< Feature > privvec
Definition: FeatureMap.h:107
FeatureMap & operator+=(const FeatureMap &rhs)
Add one feature map to another.
AnnotationState
state of identification, use getIDState() to query it
Definition: BaseFeature.h:70
void sortByPosition()
Sort features by position. Lexicographical comparison (first RT then m/z) is done.
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
Base::const_reverse_iterator ConstReverseIterator
Definition: FeatureMap.h:142
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< ProteinIdentification > protein_identifications_
protein identifications
Definition: FeatureMap.h:309
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
void swapFeaturesOnly(FeatureMap &from)
Swaps the feature content (plus its range information) of this map with the content of from...