fix biojava#344

andreasprlic · andreasprlic · commit cf1c73586550 · 2015-12-04T16:37:14.000-08:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
@@ -313,14 +313,14 @@ private CompoundSet<NucleotideCompound> getDnaCompounds() {
 			if (dnaCompounds != null) {
 				return dnaCompounds;
 			}
-			return DNACompoundSet.getDNACompoundSet();
+			return AmbiguityDNACompoundSet.getDNACompoundSet();
 		}
 
 		private CompoundSet<NucleotideCompound> getRnaCompounds() {
 			if (rnaCompounds != null) {
 				return rnaCompounds;
 			}
-			return RNACompoundSet.getRNACompoundSet();
+			return AmbiguityRNACompoundSet.getRNACompoundSet();
 		}
 
 		private CompoundSet<AminoAcidCompound> getAminoAcidCompounds() {

Original file line number	Diff line number	Diff line change
`@@ -313,14 +313,14 @@ private CompoundSet<NucleotideCompound> getDnaCompounds() {`
`313`	`313`	`if (dnaCompounds != null) {`
`314`	`314`	`return dnaCompounds;`
`315`	`315`	`}`
`316`		`- return DNACompoundSet.getDNACompoundSet();`
	`316`	`+ return AmbiguityDNACompoundSet.getDNACompoundSet();`
`317`	`317`	`}`
`318`	`318`
`319`	`319`	`private CompoundSet<NucleotideCompound> getRnaCompounds() {`
`320`	`320`	`if (rnaCompounds != null) {`
`321`	`321`	`return rnaCompounds;`
`322`	`322`	`}`
`323`		`- return RNACompoundSet.getRNACompoundSet();`
	`323`	`+ return AmbiguityRNACompoundSet.getRNACompoundSet();`
`324`	`324`	`}`
`325`	`325`
`326`	`326`	`private CompoundSet<AminoAcidCompound> getAminoAcidCompounds() {`