[Biojava-l] Re:topic about RestrictionEnzyme

[zhenqing ye]

Oups! My mistake (and apologies) about the understanding of the defination of overhangs.
thinking for a while and re-diving into the codes, George is right, maybe it's truly a bug. 
the confused codes is the following functions in RestrictionEnzyme.java
    ...
    public int getDownstreamEndType()
    {
        if (dsCutPositions[0] > dsCutPositions[1])   //if dsCutPositions[0]>dsCutPositions[1], it should be OVERHANG_3PRIME
            return OVERHANG_5PRIME;                  //to fix it, we can change the ">" to "<" or change the OVERHANG_5PRIME
        else if (dsCutPositions[0] < dsCutPositions[1])  //vice versa
            return OVERHANG_3PRIME;
        else
            return BLUNT;
    }
    ...
to ensure the judgement, the following code in the same class is right for job. so i am sorry for 
my mistake. ^_^   
    ...
    public int getUpstreamEndType() throws BioException
    {
        if (cutType == CUT_SIMPLE)
            throw new BioException(name + " does not cut upstream of the recognition site");
        if (usCutPositions[0] > usCutPositions[1])  //this is right
            return OVERHANG_5PRIME;
        else if (usCutPositions[0] < usCutPositions[1])  //this is right
            return OVERHANG_3PRIME;
        else
            return BLUNT;
    }    
    ...

thanks for George ^_^
thanks for all

zhenqing ye



---------------------------------
Do You Yahoo!?
×¢²áÊÀ½çÒ»Á÷Æ·ÖʵÄÑÅ»¢Ãâ·ÑµçÓÊ