46 #include <OpenMS/OpenMSConfig.h> 53 class ProteinIdentification;
76 private std::vector<ConsensusFeature>,
85 typedef std::vector<ConsensusFeature>
privvec;
88 using privvec::value_type;
89 using privvec::iterator;
90 using privvec::const_iterator;
91 using privvec::size_type;
92 using privvec::pointer;
93 using privvec::reference;
94 using privvec::const_reference;
95 using privvec::difference_type;
102 using privvec::resize;
103 using privvec::empty;
104 using privvec::reserve;
105 using privvec::operator[];
109 using privvec::push_back;
119 ColumnHeader(
const ColumnHeader&);
134 typedef std::vector<ConsensusFeature>
Base;
138 typedef std::vector<ConsensusFeature>::iterator
Iterator;
188 OPENMS_DLLAPI
void clear(
bool clear_meta_data =
true);
191 OPENMS_DLLAPI
const ColumnHeaders& getColumnHeaders()
const;
194 OPENMS_DLLAPI ColumnHeaders& getColumnHeaders();
197 OPENMS_DLLAPI
void setColumnHeaders(
const ColumnHeaders& column_description);
200 OPENMS_DLLAPI
const String& getExperimentType()
const;
203 OPENMS_DLLAPI
void setExperimentType(
const String& experiment_type);
212 OPENMS_DLLAPI
void sortByIntensity(
bool reverse =
false);
216 OPENMS_DLLAPI
void sortByRT();
219 OPENMS_DLLAPI
void sortByMZ();
222 OPENMS_DLLAPI
void sortByPosition();
225 OPENMS_DLLAPI
void sortByQuality(
bool reverse =
false);
228 OPENMS_DLLAPI
void sortBySize();
231 OPENMS_DLLAPI
void sortByMaps();
234 OPENMS_DLLAPI
void sortPeptideIdentificationsByMapIndex();
238 OPENMS_DLLAPI
void updateRanges()
override;
244 OPENMS_DLLAPI
const std::vector<ProteinIdentification>& getProteinIdentifications()
const;
247 OPENMS_DLLAPI std::vector<ProteinIdentification>& getProteinIdentifications();
250 OPENMS_DLLAPI
void setProteinIdentifications(
const std::vector<ProteinIdentification>& protein_identifications);
253 OPENMS_DLLAPI
const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications()
const;
256 OPENMS_DLLAPI std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications();
259 OPENMS_DLLAPI
void setUnassignedPeptideIdentifications(
const std::vector<PeptideIdentification>& unassigned_peptide_identifications);
262 OPENMS_DLLAPI
const std::vector<DataProcessing>& getDataProcessing()
const;
265 OPENMS_DLLAPI std::vector<DataProcessing>& getDataProcessing();
268 OPENMS_DLLAPI
void setDataProcessing(
const std::vector<DataProcessing>& processing_method);
271 OPENMS_DLLAPI
void setPrimaryMSRunPath(
const StringList& s);
274 OPENMS_DLLAPI
void getPrimaryMSRunPath(
StringList& toFill)
const;
295 template <
typename Type>
298 Size assignments = 0;
299 assignments += ((*this).*member_function)();
300 for (Iterator iter = this->begin(); iter != this->end(); ++iter)
302 assignments += ((*iter).*member_function)();
308 template <
typename Type>
311 Size assignments = 0;
312 assignments += ((*this).*member_function)();
313 for (ConstIterator iter = this->begin(); iter != this->end(); ++iter)
315 assignments += ((*iter).*member_function)();
std::vector< ConsensusFeature >::iterator Iterator
Mutable iterator.
Definition: ConsensusMap.h:138
A more convenient string class.
Definition: String.h:57
std::vector< ConsensusFeature >::const_reverse_iterator ConstReverseIterator
Non-mutable reverse iterator.
Definition: ConsensusMap.h:144
std::vector< PeptideIdentification > unassigned_peptide_identifications_
protein identifications
Definition: ConsensusMap.h:346
A container for consensus elements.
Definition: ConsensusMap.h:75
ColumnHeaders column_description_
Map from index to file description.
Definition: ConsensusMap.h:337
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
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:296
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< DataProcessing > data_processing_
applied data processing
Definition: ConsensusMap.h:349
Size size
Number of elements (features, peaks, ...). This is e.g. used to check for correct element indices whe...
Definition: ConsensusMap.h:127
Log Stream Class.
Definition: LogStream.h:302
std::vector< ConsensusFeature >::reverse_iterator ReverseIterator
Mutable reverse iterator.
Definition: ConsensusMap.h:142
String label
Label e.g. 'heavy' and 'light' for ICAT, or 'sample1' and 'sample2' for label-free quantitation...
Definition: ConsensusMap.h:124
std::vector< ConsensusFeature > Base
Definition: ConsensusMap.h:134
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
RangeManager< 2 > RangeManagerType
Definition: ConsensusMap.h:135
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
std::map< UInt64, ColumnHeader > ColumnHeaders
Definition: ConsensusMap.h:136
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< ProteinIdentification > protein_identifications_
protein identifications
Definition: ConsensusMap.h:343
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
std::vector< ConsensusFeature > privvec
Definition: ConsensusMap.h:85
Size applyMemberFunction(Size(Type::*member_function)() const) const
The "const" variant.
Definition: ConsensusMap.h:309
Description of the columns in a consensus map.
Definition: ConsensusMap.h:112
String filename
File name of the mzML file.
Definition: ConsensusMap.h:122
Handles the management of a position and intensity range.
Definition: RangeManager.h:47
std::vector< ConsensusFeature >::const_iterator ConstIterator
Non-mutable iterator.
Definition: ConsensusMap.h:140
Manage source document information.
Definition: DocumentIdentifier.h:55
UInt64 unique_id
Unique id of the file.
Definition: ConsensusMap.h:129