renamed OptimizeSequence to just Optimize. (#407)

* renamed OptimizeSequence to just Optimize.

Author: TimothyStiles

synthesis/codon/codon.go

@@ -46,7 +46,7 @@ File is structured as so:
   Key functions:
     TranslationTable.Translate - given a nucleic sequence string and codon table it translates sequences to UPPERCASE amino acid sequences.
 
-    TranslationTable.OptimizeSequence - 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
+    TranslationTable.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
 
     TranslationTable.UpdateWeightsWithSequence - will look at the coding regions in the given genbank data, and use those to generate new weights for the codons in the translation table. The next time a sequence is optimised, it will use those updated weights.
 
@@ -84,7 +84,7 @@ type AminoAcid struct {
 // Table is an interface encompassing what a potentially codon optimized Translation table can do
 type Table interface {
 	GetWeightedAminoAcids() []AminoAcid
-	OptimizeSequence(aminoAcids string, randomState ...int) (string, error)
+	Optimize(aminoAcids string, randomState ...int) (string, error)
 	Translate(dnaSeq string) (string, error)
 }
 
@@ -137,9 +137,9 @@ func (table *TranslationTable) GetWeightedAminoAcids() []AminoAcid {
 	return table.AminoAcids
 }
 
-// OptimizeSequence will return a set of codons which can be used to encode the given amino acid sequence. The codons
+// 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) OptimizeSequence(aminoAcids string, randomState ...int) (string, error) {
+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)

synthesis/codon/codon_test.go

@@ -78,7 +78,7 @@ func TestOptimize(t *testing.T) {
 
 	codonTable := NewTranslationTable(11)
 
-	optimizedSequence, _ := table.OptimizeSequence(gfpTranslation)
+	optimizedSequence, _ := table.Optimize(gfpTranslation)
 	optimizedSequenceTranslation, _ := codonTable.Translate(optimizedSequence)
 
 	if optimizedSequenceTranslation != gfpTranslation {
@@ -100,8 +100,8 @@ func TestOptimizeSameSeed(t *testing.T) {
 
 	randomSeed := 10
 
-	optimizedSequence, _ := optimizationTable.OptimizeSequence(gfpTranslation, randomSeed)
-	otherOptimizedSequence, _ := optimizationTable.OptimizeSequence(gfpTranslation, randomSeed)
+	optimizedSequence, _ := optimizationTable.Optimize(gfpTranslation, randomSeed)
+	otherOptimizedSequence, _ := optimizationTable.Optimize(gfpTranslation, randomSeed)
 
 	if optimizedSequence != otherOptimizedSequence {
 		t.Error("Optimized sequence with the same random seed are not the same")
@@ -117,8 +117,8 @@ func TestOptimizeDifferentSeed(t *testing.T) {
 		t.Error(err)
 	}
 
-	optimizedSequence, _ := optimizationTable.OptimizeSequence(gfpTranslation)
-	otherOptimizedSequence, _ := optimizationTable.OptimizeSequence(gfpTranslation)
+	optimizedSequence, _ := optimizationTable.Optimize(gfpTranslation)
+	otherOptimizedSequence, _ := optimizationTable.Optimize(gfpTranslation)
 
 	if optimizedSequence == otherOptimizedSequence {
 		t.Error("Optimized sequence with different random seed have the same result")
@@ -127,7 +127,7 @@ func TestOptimizeDifferentSeed(t *testing.T) {
 
 func TestOptimizeErrorsOnEmptyAminoAcidString(t *testing.T) {
 	nonEmptyCodonTable := NewTranslationTable(1)
-	_, err := nonEmptyCodonTable.OptimizeSequence("")
+	_, err := nonEmptyCodonTable.Optimize("")
 
 	if err != errEmptyAminoAcidString {
 		t.Error("Optimize should return an error if given an empty amino acid string")
@@ -137,7 +137,7 @@ func TestOptimizeErrorsOnInvalidAminoAcid(t *testing.T) {
 	aminoAcids := "TOP"
 	table := NewTranslationTable(1) // does not contain 'O'
 
-	_, optimizeErr := table.OptimizeSequence(aminoAcids)
+	_, optimizeErr := table.Optimize(aminoAcids)
 	assert.EqualError(t, optimizeErr, invalidAminoAcidError{'O'}.Error())
 }
 
@@ -298,7 +298,7 @@ func TestCapitalizationRegression(t *testing.T) {
 		t.Error(err)
 	}
 
-	optimizedSequence, _ := optimizationTable.OptimizeSequence(gfpTranslation, 1)
+	optimizedSequence, _ := optimizationTable.Optimize(gfpTranslation, 1)
 	optimizedSequenceTranslation, _ := optimizationTable.Translate(optimizedSequence)
 
 	if optimizedSequenceTranslation != strings.ToUpper(gfpTranslation) {
@@ -375,7 +375,7 @@ func TestOptimizeSequence(t *testing.T) {
 				t.Errorf("got %v, want %v", err, tt.wantUpdateWeightsErr)
 			}
 
-			got, err := optimizationTable.OptimizeSequence(tt.sequenceToOptimise, 1)
+			got, err := optimizationTable.Optimize(tt.sequenceToOptimise, 1)
 			if !errors.Is(err, tt.wantOptimiseErr) {
 				t.Errorf("got %v, want %v", err, tt.wantOptimiseErr)
 			}

synthesis/codon/example_test.go

@@ -57,13 +57,13 @@ func ExampleTranslationTable_UpdateWeights() {
 		fmt.Println("Could not update weights in example")
 	}
 
-	optimizedSequence, _ := table.OptimizeSequence(gfpTranslation, 1)
+	optimizedSequence, _ := table.Optimize(gfpTranslation, 1)
 
 	fmt.Println(optimizedSequence == sequenceWithCustomWeights)
 	// output: true
 }
 
-func ExampleTranslationTable_OptimizeSequence() {
+func ExampleTranslationTable_Optimize() {
 	gfpTranslation := "MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK*"
 
 	sequence, _ := genbank.Read("../../data/puc19.gbk")
@@ -84,7 +84,7 @@ func ExampleTranslationTable_OptimizeSequence() {
 		fmt.Println("Stop codons don't equal number of genes!")
 	}
 
-	optimizedSequence, _ := codonTable.OptimizeSequence(gfpTranslation)
+	optimizedSequence, _ := codonTable.Optimize(gfpTranslation)
 	optimizedSequenceTranslation, _ := codonTable.Translate(optimizedSequence)
 
 	fmt.Println(optimizedSequenceTranslation == gfpTranslation)

synthesis/fix/synthesis_test.go

@@ -40,7 +40,7 @@ func BenchmarkCds(b *testing.B) {
 	var functions []func(string, chan DnaSuggestion, *sync.WaitGroup)
 	functions = append(functions, RemoveSequence([]string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}, "TypeIIS restriction enzyme site."))
 	for i := 0; i < b.N; i++ {
-		seq, _ := codonTable.OptimizeSequence(phusion)
+		seq, _ := codonTable.Optimize(phusion)
 		optimizedSeq, changes, err := Cds(seq, codonTable, functions)
 		if err != nil {
 			b.Errorf("Failed to fix phusion with error: %s", err)
@@ -76,7 +76,7 @@ func TestCds(t *testing.T) {
 	phusion := "MGHHHHHHHHHHSSGILDVDYITEEGKPVIRLFKKENGKFKIEHDRTFRPYIYALLRDDSKIEEVKKITGERHGKIVRIVDVEKVEKKFLGKPITVWKLYLEHPQDVPTIREKVREHPAVVDIFEYDIPFAKRYLIDKGLIPMEGEEELKILAFDIETLYHEGEEFGKGPIIMISYADENEAKVITWKNIDLPYVEVVSSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLTIGRDGSEPKMQRIGDMTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLERVAKYSMEDAKATYELGKEFLPMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWENIVYLDFRALYPSIIITHNVSPDTLNLEGCKNYDIAPQVGHKFCKDIPGFIPSLLGHLLEERQKIKTKMKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYAVIDEEGKVITRGLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKGVKIKPGMVIGYIVLRGDGPISNRAILAEEYDPKKHKYDAEYYIENQVLPAVLRILEGFGYRKEDLRYQKTRQVGLTSWLNIKKSGTGGGGATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEKQKK*"
 	var functions []func(string, chan DnaSuggestion, *sync.WaitGroup)
 	functions = append(functions, RemoveSequence([]string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}, "TypeIIS restriction enzyme site."))
-	seq, _ := codonTable.OptimizeSequence(phusion)
+	seq, _ := codonTable.Optimize(phusion)
 	optimizedSeq, _, err := Cds(seq, codonTable, functions)
 	if err != nil {
 		t.Errorf("Failed with error: %s", err)