RE: [Biojava-l] topic about RestrictionEnzyme

george waldon gwaldon at
Wed May 11 14:30:44 EDT 2005

>From zhenqing ye:

0        (#DownstreamEndType)
24       (#DownstreamCut[0])
19       (#DownstreamCut[1])

BaeI generates 3' overhangs on both sides so DownstreamEndType equals 1 (OVERHANG_3PRIME).

Looking at the code, I just found another bug. In, the first public constructor calls the second constructor where "cutType = CUT_COMPOUND;" overwrites the attribution of cutType in the first one.

There is also a bug I found a while ago. In, around 2/3 down, put

for (Iterator ii = isoschizomers.iterator(); ii.hasNext();) {
    String isoName = (String);
    Object re = nameToEnzyme.get(isoName);

helps to deal with isoschizomers.

I had sometimes a problem with end of files in which disappears after putting mark(2):

        // end of record. Is it the last in the file?
        if(tv == null) {
          // scan for eof after whitespace
          boolean eof = false;
          while(true) {

Althought I never investigated if it was a real bug or not. Also, adding two line return at the end of the enzyme file helped.

- George

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