Make codon work with json (#4)

* Removed update weights

* add freqB table

synthesis/codon/codon.go

@@ -156,7 +156,10 @@ func (table *TranslationTable) Optimize(aminoAcids string, randomState ...int) (
 	}
 
 	var codons strings.Builder
-	codonChooser := table.Choosers
+	codonChooser, err := newAminoAcidChoosers(table.AminoAcids)
+	if err != nil {
+		return "", err
+	}
 
 	for _, aminoAcid := range aminoAcids {
 		chooser, ok := codonChooser[string(aminoAcid)]

synthesis/codon/codon_test.go

@@ -1,6 +1,7 @@
 package codon
 
 import (
+	_ "embed"
 	"errors"
 	"os"
 	"strings"
@@ -558,3 +559,20 @@ func TestUpdateWeights(t *testing.T) {
 		})
 	}
 }
+
+//go:embed default_tables/freqB.json
+var ecoliCodonTable []byte
+
+func TestCodonJSONRegression(t *testing.T) {
+	ct := ParseCodonJSON(ecoliCodonTable)
+	gfp := "MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK"
+	seed := 0
+	sequence, err := ct.Optimize(gfp, seed)
+	if err != nil {
+		t.Errorf("Failed to optimize with premade table. Got error: %s", err)
+	}
+	expectedSequence := `ATGGCATCCAAGGGCGAGGAGTTGTTCACCGGTGTTGTGCCGATCCTGGTGGAGCTGGACGGTGACGTGAACGGTCACAAATTTAGCGTGTCCGGTGAGGGTGAGGGTGATGCTACCTATGGCAAGCTGACCCTGAAATTCATTTGTACCACGGGTAAACTGCCGGTCCCGTGGCCGACGCTGGTGACCACCTTCAGCTATGGTGTGCAGTGTTTCAGCCGCTACCCGGACCACATGAAGCGCCACGACTTTTTCAAGAGCGCGATGCCGGAGGGTTATGTGCAAGAACGTACCATCAGCTTTAAAGATGATGGTAACTATAAGACCCGCGCGGAAGTCAAGTTTGAGGGTGACACGCTGGTGAATCGTATTGAGTTGAAGGGTATTGACTTTAAGGAGGATGGTAATATTTTGGGCCACAAACTGGAGTACAATTACAATAGCCACAATGTTTACATCACGGCAGATAAACAGAAGAACGGTATCAAGGCGAACTTCAAAATTCGTCACAACATTGAGGACGGTTCTGTTCAACTGGCGGACCATTACCAACAGAATACCCCGATCGGTGACGGCCCGGTTCTGCTGCCGGACAACCATTATTTGAGCACCCAGTCCGCCCTGAGCAAGGACCCGAATGAGAAGCGTGATCATATGGTTCTGCTGGAGTTTGTGACCGCGGCGGGCATCACCCACGGCATGGACGAGCTGTACAAG`
+	if sequence != expectedSequence {
+		t.Errorf("Failed to output expected sequence.")
+	}
+}