>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
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