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" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
06/22/2005 12:12 AM
Please respond to george waldon
To: Biojava-l@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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jesse
Sent: Tuesday, June 21, 2005 6:06 AM
To: biojava-l@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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