Package org.biojava.bio.alignment

Classes to generate and describe sequence alignments.

See: Description

Interface Summary

Interface	Description
Alignment	An alignment containing multiple SymbolLists.
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 Summary

Class	Description
AbstractULAlignment
Alignment.SymbolListIterator	Iterator implementation looping over symbol lists in an alignment using the labels.
AlignmentAlgorithm	This Interface provides methods for the alignment of bio-sequences.
AlignmentPair	This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.
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.
SimpleAlignment	A simple implementation of an Alignment.
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 Summary

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.

Package org.biojava.bio.alignment Description

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.