[Biojava-l] RestrictionEnzymeManager REBASE reader bug?

[mark.schreiber at novartis.com]

Hello -

This is now checked in. All tests pass (no surprise as checking for null 
never hurt anyone). This will make it into biojava1.4. If you want to add 
a test to the Junit to ensure this stays fixed it would be most 
appreciated.

I also remember some discussion a while back about the behaivour of 
certain enzymes with respect to their cleavage points which may or may not 
have been a bug. Was this ever resolved? If so does anything need fixing?

Thanks.

- Mark





"george waldon" <gwaldon at geneinfinity.org>
Sent by: biojava-l-bounces at portal.open-bio.org
06/22/2005 12:12 AM
Please respond to george waldon

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


Of course it's a bug and I reported it a while ago:

Dated from Wed 5/11/2005 11:31 AM
"There is also a bug I found a while ago. In 
RestrictionEnzymeManager.java, around 2/3 down, put

for (Iterator ii = isoschizomers.iterator(); ii.hasNext();) {
    String isoName = (String) ii.next();
    Object re = nameToEnzyme.get(isoName);
    if(re!=null)
        tempSet.add(re);
}

helps to deal with isoschizomers."

A mean to track bugs would be nice but more important I think would be a 
searchable mail archive. I remember there is a way to search biojava 
archive somewhere but I couldn't find it on the biojava web site. Would be 
nice to have a link on the site.

- George

-----Original Message-----
From: biojava-l-bounces at portal.open-bio.org 
[mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of Jesse
Sent: Tuesday, June 21, 2005 6:06 AM
To: biojava-l at biojava.org
Subject: RE: [Biojava-l] RestrictionEnzymeManager REBASE reader bug?

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
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