| 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 | 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. |