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
Block s. |
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
MultipleAlignment s 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 | 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
MultipleAlignment s. |
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. |