# Package jebl.evolution.sequences

package jebl.evolution.sequences

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 T
Codons
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 - see `Codons`.
FilteredSequence
GaplessSequence
GeneticCode
A set of standard genetic codes.
Nucleotides
Uninstantiable utility class with only static methods.
NucleotideState
Sequence
A biomolecular sequence.
Sequences
A set of sequence objects.
SequenceStateException
SequenceTester
SequenceType
Interface for sequences data types.
SequenceType.Utils
State
StateClassification
StateClassification.Default
TranslatedSequence
Utils