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 ------------------------- _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
