Hi,
I am a new user of biojava and a need help for a genBank parser.
My problem is when I try to get the location of my feature. If the location
is : join(790078..790119,791193..791337)
no problem... I can get the min, the max and both blocks.
But, if the location is : join(AC1234:790078..790119,791193..791337) the
first block describes a clone.
In this case, the first block is simply ignored and only the second block is
returned.
Here is the code I use to get this location:
while(seqI.hasNext()) {
Sequence seq = seqI.nextSequence();
this.extractFeatures(seq);
}
public void extractFeatures(Sequence seq)
throws Exception {
for (Iterator i = ((FeatureHolder)seq).features(); i.hasNext(); ) {
Feature f = (Feature) i.next();
System.out.println((f.getLocation().toString());
}
}
There is similar problems with locations like (123.567) or 123^567
It seems there is a class EmblLikeLocationParser which manages this kind of
location, but there is any public constructor and I do not know how handle
with it.
Any ideas how to get around this?
Best Regards.
Stephane.
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