| AbstractULAlignment |
|
| 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.
|
| 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.
|
| NeedlemanWunsch |
Needleman and Wunsch defined the problem of global sequence alignments, from
the first till the last symbol of a sequence.
|
| SequenceAlignment |
This Interface provides methods for the alignment of bio-sequences.
|
| SubstitutionMatrix |
This object is able to read a substitution matrix file and constructs a short
matrix in memory.
|
| UnequalLengthAlignment |
UnequalLengthAlignment has the following behavior.
|