UniqueIdIndexer< RandomAccessContainer > Class Template Reference

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>

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]

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< ConsensusMap >::resolveUniqueIdConflicts(), UniqueIdIndexer< ConsensusMap >::uniqueIdToIndex(), and UniqueIdIndexer< ConsensusMap >::updateUniqueIdToIndex().

getBase_() [2/2]

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.

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

swap()

void swap ( UniqueIdIndexer< RandomAccessContainer > &  rhs )

inline

Swap.

Note

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

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)

Note

that subordinate elements are not considered here.

updateUniqueIdToIndex()

void updateUniqueIdToIndex ( ) const

inline

Updates the hash map from unique id to index.

See also

uniqueIdToIndex()

Referenced by UniqueIdIndexer< ConsensusMap >::uniqueIdToIndex().

Member Data Documentation

uniqueid_to_index_

UniqueIdMap uniqueid_to_index_

mutableprotected

hash map from unique id to index of features

This is mutable because the hash map is updated on demand, even if the underlying container is const.

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