[Biojava-l] Strang change of Location class

Hi,

This piece of code:

//making a sequence

Alphabet dna = DNATools.getDNA();

SymbolTokenization dnaToke = dna.getTokenization("token");

SymbolList seq0 = new SimpleSymbolList(dnaToke, "ACTGGACCTAAGG");

Sequence sequence0 = new SimpleSequence(seq0, "test", "test", null);

//adding a feature with a between location
StrandedFeature.Template templ = new StrandedFeature.Template();

templ.annotation = Annotation.EMPTY_ANNOTATION;

templ.location = new BetweenLocation(new RangeLocation(7,8));

templ.source = "my feature";

templ.strand = StrandedFeature.POSITIVE;

templ.type = "interesting motif";

sequence0.createFeature(templ);

Iterator iter = sequence0.features();

while (iter.hasNext()) {

Feature feature = (Feature)iter.next();

Location location = feature.getLocation();

System.out.println("orginal feature location: " + location.getClass());

}

//converting to a simplegappedsequence
SimpleGappedSequence _sequence = new SimpleGappedSequence(sequence0);

iter = _sequence.features();

while (iter.hasNext()) {

Feature feature = (Feature)iter.next();

Location location = feature.getLocation();

System.out.println("new feature location: " + location.getClass());

}

Gives me the following output:

orginal feature location class org.biojava.bio.symbol.BetweenLocation
new feature location: class org.biojava.bio.symbol.RangeLocation

Why is the feature location changed from BetweenLocation to RangeLocation during the conversion ??

Any help would be appreciated,

David De Beule

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