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.