Package org.biojava.nbio.alignment.template
package org.biojava.nbio.alignment.template
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ClassDescriptionImplements common code for an
Alignerwhich builds a score matrix during computation.Implements common code for algorithms which compute a score.Implements a concurrency wrapper for aPairwiseSequenceAligner.Implements a concurrency wrapper for aPairwiseSequenceScorer.Implements a concurrency wrapper for aProfileProfileAligner.Defines a data structure for the gap penalties used during a sequence alignment routine.Defines the possible types of gap penalties.Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.Defines a clustering algorithm that converts a distance matrix into a tree.Defines anAlignerwhich builds a score matrix during computation.Defines an algorithm which computes a score for a sequence alignment pair picked from an alignmentProfile.Defines an algorithm which computes a score for a pair of sequences.Defines an algorithm which computes a new alignmentProfileby splitting a current alignment and realigning.Defines anAlignerfor a pair ofProfiles.Defines an algorithm which computes a score for a pairing of alignment profiles.Defines an algorithm which computes a new alignmentProfileby rescoring all pairs in an alignment and realigning.Defines an algorithm which computes a score.