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();
nvList.add(oldValue);
nvList.add(newValue);
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.
cheers,
--
-= Keith James - [EMAIL PROTECTED] - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA
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