| Package | Description |
|---|---|
| org.biojava.bio.alignment |
Classes to generate and describe sequence alignments.
|
| org.biojava.bio.structure.io |
Input and Output of Structures
|
| Class and Description |
|---|
| 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.
|
| Class and Description |
|---|
| SubstitutionMatrix
This object is able to read a substitution matrix file and constructs a short
matrix in memory.
|