[Biojava-dev] Feature at position 0

[Mark Southern]

This is a real world example.

Swissprot ID KAP3_RAT (AC P12369) is an example of a sequence with a feature
entry at sequence location 0:

FT   INIT_MET      0      0       BY SIMILARITY.


This raises an IllegalArgumentException when the sequence is read in via
SeqIOTools.fileToBiojava (see below).

I don't know how oftem this would come up but its definitely a situation
that isn't handled at the moment. Thoughts anyone?

Mark.



java.lang.IllegalArgumentException: Location 0 is outside 1..415
        at
org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:306)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
        at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAcces
sorImpl.java:39)
        at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstruc
torAccessorImpl.java:27)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:274)
        at
org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeature
Realizer.java:138)
rethrown as org.biojava.bio.BioException: Couldn't realize feature
        at
org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeature
Realizer.java:144)
        at
org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealiz
er.java:94)
        at
org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:1
98)
        at
org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:20
4)
        at
org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.
java:168)
        at
org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilde
r.java:87)
        at
org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFil
ter.java:98)
        at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:101)
        at com.exsar.test.SerializeTest.main(SerializeTest.java:24)