[Biojava-l] RestrictionEnzymeManager REBASE reader bug?

Jesse jesse-t at chello.nl
Tue Jun 21 09:06:12 EDT 2005

I think I found the problem.

The Restriction Enzyme name (<1>) of an entry can be linked to the
isoschizomers field (<2>) of other entries. So when I remove an entry, I
also have to remove those names in the isoschizomers field of other entries.

So it's not a bug.

- Jesse

-----Oorspronkelijk bericht-----
Van: mark.schreiber at novartis.com [mailto:mark.schreiber at novartis.com] 
Verzonden: dinsdag 21 juni 2005 7:46
Aan: Jesse
CC: biojava-l at biojava.org; biojava-l-bounces at portal.open-bio.org
Onderwerp: Re: [Biojava-l] RestrictionEnzymeManager REBASE reader bug?

I guess the other question I would ask is, should it crash?

By modifying the file are you fundamentally changing the format? The 
NullPointerException seems to suggest that you inserted something that 
doesn't have a matching record (or some similar problem, I'm not familiar 
with REBASE).

Try taking a look into the RestrictionEnzymeManager code at the root of 
the exception to give you some clues what might be going wrong. It's hard 
to tell if this is actually a bug or if you have incorrectly modified the 

- Mark

"Jesse" <jesse-t at chello.nl>
Sent by: biojava-l-bounces at portal.open-bio.org
06/21/2005 11:39 AM

        To:     <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] RestrictionEnzymeManager REBASE reader

Hi Mark,

With "crash" I mean an exception.

This one:
-------- Exception  ---------
Exception in thread "main" org.biojava.bio.BioError: Failed to read REBASE
data file
                 at RETools.printAllRE(RETools.java:32)
                 at RETools.main(RETools.java:15)
Caused by: java.lang.NullPointerException
                 at org.biojava.utils.SmallSet.contains(SmallSet.java:68)
                 at org.biojava.utils.SmallSet.add(SmallSet.java:81)
                 ... 3 more

OS: Microsoft Windows XP Professional SP 2 [Version 5.1.2600]
java version "1.5.0_02"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_02-b09)
Java HotSpot(TM) Client VM (build 1.5.0_02-b09, mixed mode, sharing)
BioJava: BioJava 1.4pre2

The problem I described happens when calling
RestrictionEnzymeManager.getAllEnzymes() on a modified REBASE file.
What I modified (as test) was only the name "<1>XmnI" to "<1>XmbnI" (line
35343 of REBASE format 31, version 506).

Sometimes the exception also occurs when removing some specific 
enzyme entries (from <1> to <8> including the trailing empty line).

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