[Biojava-l] topic about RestrictionEnzyme

Tue May 10 22:04:44 EDT 2005

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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