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.
Interface Summary Interface Description AlignmentAn alignment containing multiple SymbolLists. AlignmentElementAlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments. ARAlignmentARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment. EditableAlignmentEditableAlignment is an interface that defines methods for shifting bases within an Alignment. QualitativeAlignment UnequalLengthAlignmentUnequalLengthAlignment has the following behavior.
Class Summary Class Description AbstractULAlignment Alignment.SymbolListIteratorIterator implementation looping over symbol lists in an alignment using the labels. AlignmentAlgorithmThis Interface provides methods for the alignment of bio-sequences. AlignmentPairThis class stores the result of an alignment procedure that creates a pairwise alignment of two sequences. FlexibleAlignmentFlexibleAlignment 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. NeedlemanWunschNeedleman and Wunsch defined the problem of global sequence alignments, from the first till the last symbol of a sequence. SimpleAlignmentA simple implementation of an Alignment. SimpleAlignmentElementSimpleSimpleAlignment is a simple implementation of AlignmentElement. SmithWatermanSmith 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). SubstitutionMatrixThis object is able to read a substitution matrix file and constructs a short matrix in memory.
Exception Summary Exception Description IllegalAlignmentEditExceptionThe 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.