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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. |
Implementation of the Alignment
interface.
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