[Biojava-l] topic about RestrictionEnzyme

[zhenqing ye]

>BaeI generates 3' overhangs on both sides so DownstreamEndType equals 1 (OVERHANG_3PRIME).
i don't think so. you can refer the record in rebase database.
   <1>BaeI
   <2>
   <3>(10/15)ACNNNNGTAYC(12/7)
    5'                                                                          3'
     N N N N N^N N N N N N N N N N A C N N N N G T A Y C N N N N N N N N N N N N^
    ^N N N N N N N N N N N N N N N T G N N N N C A T R G N N N N N N N^N N N N N 
    3'                                                                          5'
the left side should be OVERHAND_3PRIME=1, and the right side should be OVERHAND_5PRIME=0    
the code runs ok for me. 
>I just found another bug. In RestrictionEnzyme.java, the first public constructor calls the second constructor where "cutType = CUT_COMPOUND;" overwrites the attribution of cutType in the first one.
 you can read the codes in the first constructor
 
   public RestrictionEnzyme(String name, SymbolList site,
                             int dsForward, int dsReverse)
        throws IllegalAlphabetException
    {
        this(name, site,
             null,
             new int [] { dsForward, dsReverse });
        cutType = CUT_SIMPLE;    #########it has been changed back
    }
    
the last situation you recommended, i am not very sure about it cause i have no chance to try it.
only my own opinion!
furthermore, English is not my native language. but hope it can still convey my meaning.
thanks
zhenqing ye    




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