When writing out feature qualifiers if they are db_xref values handle

jamesmorris · jamesmorris · commit 4dcfbed7987f · 2022-10-18T11:14:24.000+01:00
this differently because they don't have a value. Rather we need to use
the database and ID values to create the output
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java
@@ -24,6 +24,7 @@
 package org.biojava.nbio.core.sequence.io;
 
 import org.biojava.nbio.core.sequence.Strand;
+import org.biojava.nbio.core.sequence.features.DBReferenceInfo;
 import org.biojava.nbio.core.sequence.features.FeatureInterface;
 import org.biojava.nbio.core.sequence.features.Qualifier;
 import org.biojava.nbio.core.sequence.location.template.AbstractLocation;
@@ -127,7 +128,12 @@ protected String _write_feature(FeatureInterface<AbstractSequence<C>, C> feature
 		//Now the qualifiers...
 		for(List<Qualifier>  qualifiers : feature.getQualifiers().values()) {
 			for(Qualifier q : qualifiers){
-				line += _write_feature_qualifier(q.getName().replaceAll("%","%%"), q.getValue().replaceAll("%","%%"), q.needsQuotes());
+				if (q instanceof DBReferenceInfo) {
+					DBReferenceInfo db = (DBReferenceInfo) q;
+					line += _write_feature_qualifier(q.getName().replaceAll("%","%%"), db.getDatabase().replaceAll("%","%%") + ":" + db.getId().replaceAll("%","%%"), db.needsQuotes());	
+				} else {
+					line += _write_feature_qualifier(q.getName().replaceAll("%","%%"), q.getValue().replaceAll("%","%%"), q.needsQuotes());
+				}
 			}
 		}
 		return line;
