[Biojava-l] RestrictionEnzymeManager REBASE reader bug?

[mark.schreiber at novartis.com]

Hi -

When you say crash do you mean blue-screen-of-death type crash, 
chernobyl-type-meltdown or just a throws-an-exception and exits? If the 
latter please paste in your stack trace so we can figure out what 
happened. 

Also your JVM, OS, BioJava version would be good. Please also make sure 
you are using the latest biojava version (1.4pre2).

Thanks,

- Mark





"Jesse" <jesse-t at chello.nl>
Sent by: biojava-l-bounces at portal.open-bio.org
06/21/2005 07:36 AM

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


I found some strange things when using RestrictionEnzymeManager to get
Restriction Enzymes (RE's) from REBASE.

When I change a specific name of a RE in the REBASE file, it will crash.

Steps to prepare:
-Download the latest REBASE file from
http://rebase.neb.com/rebase/link_withrefm
-Rename it to rebase_common.dat
-Overwrite it on the default smaller rebase_common.dat which is in the
BioJava classpath org/biojava/bio/molbio/

For example:
When I change
<1>XmnI
in
<1>XmbbnI
It will crash. When I change it back again (using the same texteditor), it
will work again.

Is the RE name of the "<1>" section linked to other sections like "<2>"? 
And
then sees that a RE name is missing?

Another strange thing is that when I remove some RE enties (so from <1> to
<8> including the empty separator line after it), it will crash. Even 
though
hexeditors show that only the entry is removed and not some newline
characters etc. So the format is still the same.

Does somebody know how these problems are caused? Or did I do something
wrong?

Thanks,

Jesse




-------- Error ---------
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
-------------------------

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