Package jebl.evolution.sequences
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Interface Summary Interface Description Sequence A biomolecular sequence.Sequences A set of sequence objects.SequenceType Interface for sequences data types.StateClassification -
Class Summary Class Description AminoAcids Uninstantiable utility class with only static methods.AminoAcidState BasicSequence A default implementation of the Sequence interface.CanonicalSequence A default implementation of the Sequence interface that converts sequence characters to States such that calling getString() will always return uppercase residues with nucleotide U residues converted to TCodons CodonSequence A codon implementation of the Sequence interface.CodonState As of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - seeCodons
.FilteredSequence GaplessSequence GeneticCode A set of standard genetic codes.Nucleotides Uninstantiable utility class with only static methods.NucleotideState SequenceTester SequenceType.Utils State StateClassification.Default TranslatedSequence Utils -
Exception Summary Exception Description SequenceStateException