Method Optimize

synthesis/codon/codon.go:169–201

Optimize will return a set of codons which can be used to encode the given amino acid sequence. The codons picked are weighted according to the computed translation table's weights

(aminoAcids string, randomState ...int)

// Optimize will return a set of codons which can be used to encode the given amino acid sequence. The codons
// picked are weighted according to the computed translation table's weights
func (table *TranslationTable) Optimize(aminoAcids string, randomState ...int) (string, error) {
	// Finding any given aminoAcid is dependent upon it being capitalized, so
	// we do that here.
	aminoAcids = strings.ToUpper(aminoAcids)

	if len(aminoAcids) == 0 {
		return "", errEmptyAminoAcidString
	}

	// weightedRand library insisted setting seed like this. Not sure what environmental side effects exist.
	var randomSource rand.Source
	if len(randomState) > 0 {
		randomSource = rand.NewSource(int64(randomState[0]))
	} else {
		randomSource = rand.NewSource(time.Now().UTC().UnixNano())
	}
	rand := rand.New(randomSource)

	var codons strings.Builder
	codonChooser := table.Choosers

	for _, aminoAcid := range aminoAcids {
		chooser, ok := codonChooser[string(aminoAcid)]
		if !ok {
			return "", invalidAminoAcidError{aminoAcid}
		}
		codon := chooser.PickSource(rand)

		codons.WriteString(codon.(string))
	}

	return codons.String(), nil
}

// UpdateWeights will update the translation table's codon pickers with the given amino acid codon weights
func (table *TranslationTable) UpdateWeights(aminoAcids []AminoAcid) error {