Package jebl.evolution.sequences

Interface Summary

Sequence	A biomolecular sequence.
Sequences	A set of sequence objects.
SequenceType	Interface for sequences data types.
StateClassification

Class Summary

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 T
Codons
CodonState	As of 2007-07-30, instances of this class are only constructed for non-ambigous nucleotide triplets - see Codons.
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

SequenceStateException