[Biojava-l] SimpleSequenceBuilder behaviour

Keith James kdj@sanger.ac.uk
27 Mar 2001 11:11:39 +0100

Someone has just pointed out to me that the behaviour of the
SimpleSequenceBuilder with respect to FeatureProperties has changed
when adding new properties. In addProperty():

if (oldValue != null) {
    if (oldValue instanceof String) {
	newValue = ((String) oldValue) + " " + newValue.toString();
    } else {
	if (oldValue instanceof Collection) {
	    ((Collection) oldValue).add(newValue);
	    newValue = oldValue;
	} else {
	    List nvList = new ArrayList();
	    newValue = nvList;

So Strings are a special case and are being (unexpectedly, for us)
concatenated. This means that EMBL/Genbank features with multiple,
say, /gene qualifiers are having them mangled.

If I remove the first 3 lines of this block, things will work
again. But would that break anything else?

The alternative is for the parsers to keep a check of what qualifier
keys have been sent to the listener and always supply the first value
String wrapped in a List, then subsequent values as Strings, which is
a hack likely to break again later.



-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA