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 that fulfill the following conditions:
BlockSet	A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment as a collection of Blocks.
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.).
MultipleSuperimposer
ScoresCache	Interface for classes which implement a temporary cache for various numeric scores, e.g.

Class Summary

Class	Description
AbstractScoresCache
BlockImpl	General implementation of a Block that supports alignments with gaps.
BlockSetImpl	A general implementation of a BlockSet to store multiple alignments.
MultipleAlignmentEnsembleImpl	A general implementation of a MultipleAlignmentEnsemble.
MultipleAlignmentImpl	A general implementation of a MultipleAlignment.
MultipleAlignmentScorer	Utility class for calculating common scores of MultipleAlignments.
MultipleAlignmentTools	Utility functions for working with MultipleAlignment.
MultipleAlignmentWriter	This class contains functions for the conversion of MultipleAlignment to various String outputs.
ReferenceSuperimposer	Superimposes each structure in a MultipleAlignment onto a reference structure.