A design-related question: In GenbankSequenceDB's getSequence() method, the exception-handling code when catching an Exception thrown when a bad accession is used to search (returning nothing from Genbank) prints an error to STDOUT rather than passing the Exception up the chain like a good little Java method should:
...
} catch (Exception e) {
System.out.println("Exception found in GenbankSequenceDB -- getSequence");
System.out.println(e.toString());
ExceptionFound = true;
IOExceptionFound = true;
return null;
}
Is there a reason behind this? It results in an application that prints to STDOUT regardless of my wishes and also limits my ability to catch the Exception myself higher up in the stack to deal with it in an application-specific way. Just curious ... thanks.
-j
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