| AbstractMolecularSequence | A molecular sequence is defined by its symbols only : two instances holding the same symbols are interchangeable, so the class carries no identity and exposes no setter. Every transformation returns a brand new instance. |
| AbstractNucleicSequence | Holds what DNA and RNA have in common : a complement table covering the IUPAC degenerated symbols, and the GC content. |
| AminoAcidSequence | Accepts the twenty amino acids in single-letter format, plus the two symbols already handled by SequenceManager::charge() and SequenceManager::chemicalGroup() : X for an unknown residue and the asterisk for a stop codon. |
| DnaSequence | Accepts the four deoxyribonucleotides and the IUPAC degenerated symbols already tolerated by SequenceTrait::cleanSequence(). |
| InvalidSequenceException | Class InvalidSequenceException |
| MolecularSequenceFactory | The molecule type stored by the parsers is the raw one of the source file : "mRNA" or "ss-DNA" for GenBank and EMBL, "PRT;" for Swiss-Prot. This factory maps those to the matching value object instead of leaving the caller compare strings. |
| RnaSequence | Accepts the four ribonucleotides and the IUPAC degenerated symbols already tolerated by SequenceTrait::cleanSequence(). |