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