## Package org.biojava.bio.alignment

Implementation of the `Alignment` interface.

See:
Description

Interface Summary
AlignmentElement: AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.
ARAlignment: ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
EditableAlignment: EditableAlignment is an interface that defines methods for shifting bases within an Alignment.
QualitativeAlignment
UnequalLengthAlignment: UnequalLengthAlignment has the following behavior.

Class Summary
AbstractULAlignment
FlexibleAlignment: FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment.
SimpleAlignmentElement: SimpleSimpleAlignment is a simple implementation of AlignmentElement.

Exception Summary
IllegalAlignmentEditException: The usual reason for throwing an IllegalAlignmentEditException is that you are trying to shift a group of bases in such a way that it would require deleting bases.

## Package org.biojava.bio.alignment Description

Implementation of the `Alignment` interface.