See: Description
Interface | Description |
---|---|
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 | Description |
---|---|
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.
|
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.
|
SimpleAlignmentElement |
SimpleSimpleAlignment is a simple implementation of
AlignmentElement.
|
SmithWaterman |
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).
|
SubstitutionMatrix |
This object is able to read a substitution matrix file and constructs a short
matrix in memory.
|
Exception | Description |
---|---|
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.
|
Classes to generate and describe sequence alignments.
Classes can represent alignments of one or more sequences. Gaps and unequal
alignments can be represented. Quality can be represented using
QualitativeAlignment
. Additionally implementations of the Needleman-
Wunsch and Smith-Waterman algorithms are provided.