OpenMS
ParentSequence Struct Reference

Representation of a parent sequence that is identified only indirectly (e.g. a protein). More...

#include <OpenMS/METADATA/ID/ParentSequence.h>

Inheritance diagram for ParentSequence:
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Collaboration diagram for ParentSequence:
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Public Member Functions

 ParentSequence (const String &accession, MoleculeType molecule_type=MoleculeType::PROTEIN, const String &sequence="", const String &description="", double coverage=0.0, bool is_decoy=false, const AppliedProcessingSteps &steps_and_scores=AppliedProcessingSteps())
 
 ParentSequence (const ParentSequence &)=default
 
ParentSequencemerge (const ParentSequence &other)
 
- Public Member Functions inherited from ScoredProcessingResult
AppliedProcessingSteps::nth_index< 1 >::type & getStepsAndScoresByStep ()
 Return the applied processing steps (incl. scores) as a set ordered by processing step reference (option) More...
 
const AppliedProcessingSteps::nth_index< 1 >::type & getStepsAndScoresByStep () const
 Return the applied processing steps (incl. scores) as a set ordered by processing step reference (option) - const variant. More...
 
void addProcessingStep (const AppliedProcessingStep &step)
 Add an applied processing step. More...
 
void addProcessingStep (ProcessingStepRef step_ref, const std::map< ScoreTypeRef, double > &scores=std::map< ScoreTypeRef, double >())
 Add a processing step (and associated scores, if any) More...
 
void addScore (ScoreTypeRef score_type, double score, const std::optional< ProcessingStepRef > &processing_step_opt=std::nullopt)
 Add a score (possibly connected to a processing step) More...
 
ScoredProcessingResultmerge (const ScoredProcessingResult &other)
 Merge in data from another object. More...
 
std::pair< double, bool > getScore (ScoreTypeRef score_ref) const
 Look up a score by score type. More...
 
std::pair< double, bool > getScore (ScoreTypeRef score_ref, std::optional< ProcessingStepRef > processing_step_opt) const
 Look up a score by score type and processing step. More...
 
std::tuple< double, std::optional< ProcessingStepRef >, bool > getScoreAndStep (ScoreTypeRef score_ref) const
 Look up a score and associated processing step by score type. More...
 
std::tuple< double, std::optional< ScoreTypeRef >, bool > getMostRecentScore () const
 Get the (primary) score from the most recent processing step. More...
 
Size getNumberOfScores () const
 Return the number of scores associated with this result. More...
 
- Public Member Functions inherited from MetaInfoInterface
 MetaInfoInterface ()
 Constructor. More...
 
 MetaInfoInterface (const MetaInfoInterface &rhs)
 Copy constructor. More...
 
 MetaInfoInterface (MetaInfoInterface &&) noexcept
 Move constructor. More...
 
 ~MetaInfoInterface ()
 Destructor. More...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (MetaInfoInterface &&) noexcept
 Move assignment operator. More...
 
void swap (MetaInfoInterface &rhs)
 Swap contents. More...
 
bool operator== (const MetaInfoInterface &rhs) const
 Equality operator. More...
 
bool operator!= (const MetaInfoInterface &rhs) const
 Equality operator. More...
 
const DataValuegetMetaValue (const String &name) const
 Returns the value corresponding to a string, or DataValue::EMPTY if not found. More...
 
DataValue getMetaValue (const String &name, const DataValue &default_value) const
 Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found. More...
 
const DataValuegetMetaValue (UInt index) const
 Returns the value corresponding to the index, or DataValue::EMPTY if not found. More...
 
DataValue getMetaValue (UInt index, const DataValue &default_value) const
 Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found. More...
 
bool metaValueExists (const String &name) const
 Returns whether an entry with the given name exists. More...
 
bool metaValueExists (UInt index) const
 Returns whether an entry with the given index exists. More...
 
void setMetaValue (const String &name, const DataValue &value)
 Sets the DataValue corresponding to a name. More...
 
void setMetaValue (UInt index, const DataValue &value)
 Sets the DataValue corresponding to an index. More...
 
void removeMetaValue (const String &name)
 Removes the DataValue corresponding to name if it exists. More...
 
void removeMetaValue (UInt index)
 Removes the DataValue corresponding to index if it exists. More...
 
void addMetaValues (const MetaInfoInterface &from)
 function to copy all meta values from one object to this one More...
 
void getKeys (std::vector< String > &keys) const
 Fills the given vector with a list of all keys for which a value is set. More...
 
void getKeys (std::vector< UInt > &keys) const
 Fills the given vector with a list of all keys for which a value is set. More...
 
bool isMetaEmpty () const
 Returns if the MetaInfo is empty. More...
 
void clearMetaInfo ()
 Removes all meta values. More...
 

Public Attributes

String accession
 
enum MoleculeType molecule_type
 
String sequence
 
String description
 
double coverage
 sequence coverage as a fraction between 0 and 1 More...
 
bool is_decoy
 
- Public Attributes inherited from ScoredProcessingResult
AppliedProcessingSteps steps_and_scores
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 Returns a reference to the MetaInfoRegistry. More...
 
- Protected Member Functions inherited from ScoredProcessingResult
 ScoredProcessingResult (const AppliedProcessingSteps &steps_and_scores=AppliedProcessingSteps())
 Constructor. More...
 
 ScoredProcessingResult (const ScoredProcessingResult &)=default
 Copy c'tor. More...
 
- Protected Member Functions inherited from MetaInfoInterface
void createIfNotExists_ ()
 Creates the MetaInfo object if it does not exist. More...
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) More...
 

Detailed Description

Representation of a parent sequence that is identified only indirectly (e.g. a protein).

Constructor & Destructor Documentation

◆ ParentSequence() [1/2]

ParentSequence ( const String accession,
MoleculeType  molecule_type = MoleculeType::PROTEIN,
const String sequence = "",
const String description = "",
double  coverage = 0.0,
bool  is_decoy = false,
const AppliedProcessingSteps steps_and_scores = AppliedProcessingSteps() 
)
inlineexplicit

◆ ParentSequence() [2/2]

ParentSequence ( const ParentSequence )
default

Member Function Documentation

◆ merge()

Member Data Documentation

◆ accession

◆ coverage

double coverage

sequence coverage as a fraction between 0 and 1

Referenced by IdentificationDataConverter::exportParentSequenceToMzTab_().

◆ description

◆ is_decoy

bool is_decoy

Referenced by ParentSequence::merge().

◆ molecule_type

enum MoleculeType molecule_type

◆ sequence