[Biojava-l] Errors to STDOUT in BioJava?

James Diggans jdiggans at excelsiortech.com
Sat Nov 20 23:12:49 EST 2004

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 -- 
       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.

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