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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Verzonden: dinsdag 21 juni 2005 7:46 Aan: Jesse CC: biojava-l@biojava.org; [EMAIL PROTECTED] 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 file. - Mark "Jesse" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 06/21/2005 11:39 AM To: <biojava-l@biojava.org> cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] RestrictionEnzymeManager REBASE reader bug? 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 org.biojava.bio.molbio.RestrictionEnzymeManager.loadData(RestrictionEnzymeMa nager.java:415) at org.biojava.bio.molbio.RestrictionEnzymeManager.<clinit>(RestrictionEnzymeMa nager.java:136) 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) at org.biojava.bio.molbio.RestrictionEnzymeManager.loadData(RestrictionEnzymeMa nager.java:407) ... 3 more ------------------------- OS: Microsoft Windows XP Professional SP 2 [Version 5.1.2600] Java: 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 restriction enzyme entries (from <1> to <8> including the trailing empty line). _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
