[Biojava-l] topic about RestrictionEnzyme

[mark.schreiber at novartis.com]

I was going to patch this in CVS but it seems Richard beat me to it! 

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





zhenqing ye <yezhenqing at yahoo.com.cn>
Sent by: biojava-l-bounces at portal.open-bio.org
05/11/2005 10:04 AM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] topic about RestrictionEnzyme


Hi,
  i have solved the problem, so let's share it.
 
  the code line in RestrictionEnzymeManager.java should be changed to the 
correct one
  as following.
 
            ....
            // Create site value splitter
            RegexSplitter site =
                new 
RegexSplitter(Pattern.compile("(\\(-?\\d/-?\\d+\\)|[A-Za-z^]+)"), 1); # 
old one
            ... 
 
                new 
RegexSplitter(Pattern.compile("(\\(-?\\d+/-?\\d+\\)|[A-Za-z^]+)"), 1); # 
new one 
 
  just add one "+" character. hoho, i think it's a mini incaution, not 
bug.
 
  furthermore, something in my previous draft should be changed too.
 
     0        (#DownstreamEndType)              0 (#DownstreamEndType)
     12       (#DownstreamCut[0])      ----->   24 (#DownstreamCut[0])
     7        (#DownstreamCut[1])               19 (#DownstreamCut[1])
 
        Bsp24I
                          5'      ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^   3'
                          3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^        5'
 
       length(GACNNNNNNTGGNNNNNNNNNNNN)=24
       length(CTGNNNNNNACCNNNNNNN)=19 
 
 thanks
 
 zhenqing ye 



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