This is strange. We do use the merging annotation stuff extensively inside biojava, so I'm not quite sure what is going on here. Could you send a small program (or your complete program if you can't be bothered to cut it down) so that we can sort this out?
Matthew
Karin Lagesen wrote:
I try to use a MergeAnnotation object to merge the annotation of two
features. This I do like this:
MergeAnnotation mergeAnn = new MergeAnnotation();
mergeAnn.addAnnotation(before.getAnnotation());
mergeAnn.addAnnotation(after.getAnnotation());
This mergeAnn object is then used in a SequenceFactory to make a
feature of the sequence in between two sequences.
I have however come across a curious problem. When I try to list all
the features in this MergeAnnotation like this:
Annotation seqAn = f.getAnnotation();
for (Iterator it = seqAn.keys().iterator(); it.hasNext();) {
Object key = it.next();
Object value = seqAn.getProperty(key);
annotation += (key.toString() + ": " + value.toString());
}
I get this error message:
Exception in thread "main" java.util.NoSuchElementException: Can't
find property [description_line, description] at org.biojava.bio.MergeAnnotation.getProperty(MergeAnnotation.java:110)
at no.uio.labmed.intergene.ProcessFiles.process(Unknown Source)
at no.uio.labmed.InterGene.main(Unknown Source)
When I do a tostring on the key, I get this:
Key [description_line, description]
It seems like in a MergeAnnotation object the key becomes composed
of both the key and the property of that key. Is this how it is
supposed to be, am I misunderstanding things, or is this a bug?
TIA,
Karin
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