Package org.biojava.nbio.core.alignment.template
package org.biojava.nbio.core.alignment.template
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ClassDescriptionDefines a data structure for a
Sequencewithin an alignment.Defines an alignment step in order to pass alignment information from anAlignerto a constructor.Defines a mutable (editable) data structure for anAlignedSequence.Defines a mutable (editable) data structure for aProfile.Defines a mutable (editable) data structure for aProfilePair.Defines a mutable (editable) data structure for the results of pairwise sequence alignment.Defines a data structure for the results of sequence alignment.List of output formats.Defines a data structure for the results of the alignment of a pair ofProfiles.Defines a data structure for a view of sequence alignment.Defines a data structure for the results of pairwise sequence alignment.SubstitutionMatrix<C extends Compound>Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of oneCompoundin a sequence for another.