35 #ifndef OPENMS_KERNEL_CONSENSUSMAP_H
36 #define OPENMS_KERNEL_CONSENSUSMAP_H
54 class ProteinIdentification;
73 private std::vector<ConsensusFeature>,
82 typedef std::vector<ConsensusFeature>
privvec;
85 using privvec::value_type;
86 using privvec::iterator;
87 using privvec::const_iterator;
88 using privvec::size_type;
89 using privvec::pointer;
90 using privvec::reference;
91 using privvec::const_reference;
92 using privvec::difference_type;
99 using privvec::resize;
100 using privvec::empty;
101 using privvec::reserve;
102 using privvec::operator[];
106 using privvec::push_back;
116 FileDescription(
const FileDescription&);
131 typedef std::vector<ConsensusFeature>
Base;
135 typedef std::vector<ConsensusFeature>::iterator
Iterator;
175 OPENMS_DLLAPI
void clear(
bool clear_meta_data =
true);
253 OPENMS_DLLAPI
void setDataProcessing(
const std::vector<DataProcessing>& processing_method);
274 template <
typename Type>
277 Size assignments = 0;
278 assignments += ((*this).*member_function)();
279 for (
Iterator iter = this->begin(); iter != this->end(); ++iter)
281 assignments += ((*iter).*member_function)();
287 template <
typename Type>
290 Size assignments = 0;
291 assignments += ((*this).*member_function)();
292 for (
ConstIterator iter = this->begin(); iter != this->end(); ++iter)
294 assignments += ((*iter).*member_function)();
336 #endif // OPENMS_KERNEL_CONSENSUSMAP_H
void setDataProcessing(const std::vector< DataProcessing > &processing_method)
sets the description of the applied data processing
std::vector< ConsensusFeature >::iterator Iterator
Mutable iterator.
Definition: ConsensusMap.h:135
void sortByMZ()
Sorts the peaks to m/z position.
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
A more convenient string class.
Definition: String.h:57
void clear(bool clear_meta_data=true)
Clears all data and meta data.
String label
Label e.g. 'heavy' and 'light' for ICAT, or 'sample1' and 'sample2' for label-free quantitation...
Definition: ConsensusMap.h:121
std::vector< ConsensusFeature >::const_reverse_iterator ConstReverseIterator
Non-mutable reverse iterator.
Definition: ConsensusMap.h:141
Source file description for input files.
Definition: ConsensusMap.h:109
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
std::vector< PeptideIdentification > unassigned_peptide_identifications_
protein identifications
Definition: ConsensusMap.h:325
const FileDescriptions & getFileDescriptions() const
Non-mutable access to the file descriptions.
UInt64 unique_id
Unique id of the file.
Definition: ConsensusMap.h:126
A container for consensus elements.
Definition: ConsensusMap.h:72
void sortByQuality(bool reverse=false)
Sorts the peaks according to ascending quality.
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:275
std::vector< DataProcessing > data_processing_
applied data processing
Definition: ConsensusMap.h:328
void setExperimentType(const String &experiment_type)
Mutable access to the experiment type.
ConsensusMap()
Default constructor.
Log Stream Class.
Definition: LogStream.h:303
~ConsensusMap()
Destructor.
const String & getExperimentType() const
Non-mutable access to the experiment type.
FileDescriptions file_description_
Map from index to file description.
Definition: ConsensusMap.h:316
std::vector< ConsensusFeature >::reverse_iterator ReverseIterator
Mutable reverse iterator.
Definition: ConsensusMap.h:139
String experiment_type_
type of experiment (label-free, itraq, ...); see xsd schema
Definition: ConsensusMap.h:319
std::vector< ConsensusFeature > Base
Definition: ConsensusMap.h:131
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
void sortByMaps()
Sorts with respect to the sets of maps covered by the consensus features (lexicographically).
A base class for random access containers for classes derived from UniqueIdInterface that adds functi...
Definition: UniqueIdIndexer.h:64
void setFileDescriptions(const FileDescriptions &file_description)
Mutable access to the file descriptions.
RangeManager< 2 > RangeManagerType
Definition: ConsensusMap.h:132
void setUnassignedPeptideIdentifications(const std::vector< PeptideIdentification > &unassigned_peptide_identifications)
sets the unassigned peptide identifications
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:71
std::map< UInt64, FileDescription > FileDescriptions
Definition: ConsensusMap.h:133
A base class defining a common interface for all classes having a unique id.
Definition: UniqueIdInterface.h:52
const std::vector< DataProcessing > & getDataProcessing() const
returns a const reference to the description of the applied data processing
std::vector< ProteinIdentification > protein_identifications_
protein identifications
Definition: ConsensusMap.h:322
ConsensusMap & operator=(const ConsensusMap &source)
Assignment operator.
void sortBySize()
Sorts with respect to the size (number of elements)
std::vector< ConsensusFeature > privvec
Definition: ConsensusMap.h:82
void swap(ConsensusMap &from)
Swaps the content of this map with the content of from.
bool isMapConsistent(Logger::LogStream *stream=0) const
checks if the given maps are unique and all FeatureHandles actually refer to a registered map ...
bool operator==(const ConsensusMap &rhs) const
Equality operator.
bool operator!=(const ConsensusMap &rhs) const
Equality operator.
void sortByPosition()
Lexicographically sorts the peaks by their position (First RT then m/z).
Handles the management of a position and intensity range.
Definition: RangeManager.h:48
void updateRanges()
Updates minimum and maximum position/intensity.
std::vector< ConsensusFeature >::const_iterator ConstIterator
Non-mutable iterator.
Definition: ConsensusMap.h:137
String filename
File name of the file.
Definition: ConsensusMap.h:119
Size size
Number of elements (features, peaks, ...). This is e.g. used to check for correct element indices whe...
Definition: ConsensusMap.h:124
void setProteinIdentifications(const std::vector< ProteinIdentification > &protein_identifications)
sets the protein identifications
void sortByRT()
Sorts the peaks to RT position.
ConsensusMap & operator+=(const ConsensusMap &rhs)
Add one consensus map to another.
Manage source document information.
Definition: DocumentIdentifier.h:56
void sortByIntensity(bool reverse=false)
Sorts the peaks according to ascending intensity.
Size applyMemberFunction(Size(Type::*member_function)() const) const
The "const" variant.
Definition: ConsensusMap.h:288