Package org.biojava.nbio.structure.align.multiple

Interface Summary

Interface	Description
Block	A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a sequential order.
BlockSet	A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.
MultipleAlignment	A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type.
MultipleAlignmentEnsemble	A MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm, version, creation time, etc.).
ScoresCache	Interface for classes which implement a temporary cache for various numeric scores, e.g.

Class Summary

Class	Description
AbstractScoresCache	Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.
BlockImpl	General implementation of a Block that supports any type of sequential alignment with gaps.
BlockSetImpl	A general implementation of a BlockSet to store a flexible part of a multiple alignment.
MultipleAlignmentEnsembleImpl	A general implementation of a MultipleAlignmentEnsemble.
MultipleAlignmentImpl	A general implementation of a MultipleAlignment.