A base class for random access containers for classes derived from UniqueIdInterface that adds functionality to convert a unique id into an index into the container. More...

#include <OpenMS/CONCEPT/UniqueIdIndexer.h>

Inheritance diagram for UniqueIdIndexer< RandomAccessContainer >:

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Collaboration diagram for UniqueIdIndexer< RandomAccessContainer >:

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Public Types
typedef boost::unordered_map< UInt64, Size >	UniqueIdMap

Public Member Functions
Size	uniqueIdToIndex (UInt64 unique_id) const
	Returns the index of the feature with the given unique id, or Size(-1) if none exists in this random access container. More...

void	updateUniqueIdToIndex () const
	Updates the hash map from unique id to index. More...

Size	resolveUniqueIdConflicts ()
	Assign new UID's to doubly occurring UID's. More...

void	swap (UniqueIdIndexer &rhs)
	Swap. More...

Protected Member Functions
const RandomAccessContainer &	getBase_ () const
	A little helper to get access to the base (!) class RandomAccessContainer. More...

RandomAccessContainer &	getBase_ ()
	A little helper to get access to the base (!) class RandomAccessContainer. More...

Protected Attributes
UniqueIdMap	uniqueid_to_index_
	hash map from unique id to index of features More...

Detailed Description

template<typename RandomAccessContainer>
class OpenMS::UniqueIdIndexer< RandomAccessContainer >

A base class for random access containers for classes derived from UniqueIdInterface that adds functionality to convert a unique id into an index into the container.

See FeatureMap and ConsensusMap for living examples. The RandomAccessContainer must support operator[], at(), and size().

Member Typedef Documentation

◆ UniqueIdMap

typedef boost::unordered_map<UInt64, Size> UniqueIdMap

Member Function Documentation

◆ getBase_() [1/2]

RandomAccessContainer& getBase_ ( )

inlineprotected

A little helper to get access to the base (!) class RandomAccessContainer.

This is just a static_cast and probably not interesting elsewhere, so we make it a protected member.

◆ getBase_() [2/2]

const RandomAccessContainer& getBase_ ( ) const

inlineprotected

A little helper to get access to the base (!) class RandomAccessContainer.

This is just a static_cast and probably not interesting elsewhere, so we make it a protected member.

Referenced by UniqueIdIndexer< RandomAccessContainer >::resolveUniqueIdConflicts(), UniqueIdIndexer< RandomAccessContainer >::uniqueIdToIndex(), and UniqueIdIndexer< RandomAccessContainer >::updateUniqueIdToIndex().

◆ resolveUniqueIdConflicts()

Size resolveUniqueIdConflicts ( )

inline

Assign new UID's to doubly occurring UID's.

Assign new UID's to non-unique UID's. This usually occurs in merging of 'old' feature files, which have sequentially increasing UID's. Conflicting entries receive a new UID, such that all UID's are unique in the container.

Note: Subordinate features are not checked and may remain non-unique. However, they are associated to their parent which makes identification 'unique'.

Returns: The number of invalid (=replaced) elements

References UniqueIdIndexer< RandomAccessContainer >::getBase_(), UniqueIdInterface::isValid(), and UniqueIdIndexer< RandomAccessContainer >::uniqueid_to_index_.

◆ swap()

void swap ( UniqueIdIndexer< RandomAccessContainer > & rhs )

inline

Swap.

Note: obviously we can swap only with indices for the same type.

References UniqueIdIndexer< RandomAccessContainer >::uniqueid_to_index_.

◆ uniqueIdToIndex()

Size uniqueIdToIndex ( UInt64 unique_id ) const

inline

Returns the index of the feature with the given unique id, or Size(-1) if none exists in this random access container.

The complexity is expected constant upon success, linear upon failure.

The lookup actually performs the following steps:

consult the internal hash map (i.e., uniqueid_to_index_)
if an index is found and that element indeed has this unique id, then return the index
if no index is found or the unique ids do not match, then update the hash map (using updateUniqueIdToIndex()) and lookup the index again
if an index is found this time, return it, otherwise return Size(-1)