Uses of Package
org.biojava.nbio.alignment.routines

Packages that use org.biojava.nbio.alignment.routines

Package	Description
org.biojava.nbio.alignment
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template

Classes in org.biojava.nbio.alignment.routines used by org.biojava.nbio.alignment

Class and Description
AnchoredPairwiseSequenceAligner This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.

Classes in org.biojava.nbio.alignment.routines used by org.biojava.nbio.alignment.routines

Class and Description
AlignerHelper.Anchor Compounds in query and target sequences that must align
AlignerHelper.Cut Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
AlignerHelper.Last Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence).
AlignerHelper.Subproblem Alignment subproblem.
AnchoredPairwiseSequenceAligner This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.

Classes in org.biojava.nbio.alignment.routines used by org.biojava.nbio.alignment.template

Class and Description
AlignerHelper.Anchor Compounds in query and target sequences that must align
AlignerHelper.Subproblem Alignment subproblem.