Uses of Package
org.biojava.bio.alignment

Packages that use org.biojava.bio.alignment

org.biojava.bio.alignment

Classes to generate and describe sequence alignments.

Classes in org.biojava.bio.alignment used by org.biojava.bio.alignment

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 definied 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 biosequences.

SubstitutionMatrix
This object is able to read a substitution matrix file and constructs an int matrix to store the matrix.

UnequalLengthAlignment
UnequalLengthAlignment has the following behavior.