AccessionID

Used in Sequences as the unique indentifier.

BasicSequence<C extends Compound>

Bare bones version of the Sequence object to be used sparingly.

CDSComparator   CDSSequence

Represents a exon or coding sequence in a gene.

ChromosomeSequence

A ChromosomeSequence is a DNASequence but keeps track of geneSequences

DNASequence

This is class should model the attributes associated with a DNA sequence

ExonComparator

Sort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction.

ExonSequence

A gene contains a collection of Exon sequences

GeneSequence   IntronSequence   MultipleSequenceAlignment<S extends Sequence<C>,​C extends Compound>

Implements a minimal data structure for reading and writing a sequence alignment.

ProteinSequence

The representation of a ProteinSequence

RNASequence

RNASequence where RNACompoundSet are the allowed values

SequenceComparator

Used to sort sequences

SequenceOptimizationHints

A static class that provides optimization hints for memory or performance handling of sequence data.

StartCodonSequence

Used to map the start codon feature on a gene

StopCodonSequence

Used to map the stop codon sequence on a gene

TaxonomyID

A sequence can be associated with a species or Taxonomy ID

TranscriptSequence

This is the sequence if you want to go from a gene sequence to a protein sequence.