RE: [Biojava-l] topic about RestrictionEnzyme

[george waldon]

>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 RestrictionEnzyme.java, 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 RestrictionEnzymeManager.java, around 2/3 down, put

for (Iterator ii = isoschizomers.iterator(); ii.hasNext();) {
    String isoName = (String) ii.next();
    Object re = nameToEnzyme.get(isoName);
    if(re!=null)
        tempSet.add(re);
}

helps to deal with isoschizomers.

I had sometimes a problem with end of files in org.biojava.bio.program.tagvalue.Parser.java 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) {
            reader.mark(2);

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