[Biojava-l] RestrictionEnzymeManager REBASE reader bug?

[Jesse]

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).