If you have a Sequence object and want a sub-sequence, use SequenceTools.subSequence() to extract part of it. This will take care of all the attached features as well. To get the symbols for a feature, call f.getSymbols(). This will take care of reverse-complementing symbols that have a reverse strand.
In what way is subStr returning the wrong information? Could you provide an example?
Matthew
Y D Sun wrote:
Dear all,
Is there a method in BioJava that returns a sub-sequence using a Location parameter (not subStr() or subList() with two integers - start and end)? This consideration comes from my requirement to get the nucleotide sub-sequence corresponding to a CDS section. In such a case, the subStr(start, end) method cannot always return the sub-sequence correctly.
Thanks.
George
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