Package org.biojava.bio.alignment
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.
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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.