All Classes and Interfaces
Class
Description
This Interface provides methods for the alignment of bio-sequences.
AlignmentElement is a class which represents a SymbolList and its
location within an Alignment This is for use in
UnequalLengthAlignments and ARAlignments.
This class stores the result of an alignment procedure that creates a
pairwise alignment of two sequences.
ARAlignment is an interface that defines methods for adding and
removing seqeunces from an Alignment.
EditableAlignment is an interface that defines methods for
shifting bases within an Alignment.
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.
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.
Needleman and Wunsch defined the problem of global sequence alignments, from
the first till the last symbol of a sequence.
SimpleSimpleAlignment is a simple implementation of
AlignmentElement.
Smith and Waterman developed an efficient dynamic programming algorithm to
perform local sequence alignments, which returns the most conserved region of
two sequences (longest common substring with modifications).
This object is able to read a substitution matrix file and constructs a short
matrix in memory.
UnequalLengthAlignment has the following behavior.