[Biojava-l] RestrictionEnzymeManager REBASE reader bug?

[Jesse]

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
-------------------------