[Biojava-l] Errors to STDOUT in BioJava?

[j vermont]

hello all,

I asked JD if a proper solution to this would be to rethrow Exception as 
such:

} catch (Exception e) {
>       System.out.println("Exception found in GenbankSequenceDB -- 
>getSequence");
>       System.out.println(e.toString());
>       ExceptionFound = true;
>       IOExceptionFound = true;
         //create instance of Exception and throw it here so it gets passed 
back up the stack to
         // the calling method....
         Exception myException = new Exception("bad accession error");
         throw myException;
>       return null;
>     }

the compiler won't complain if you're not throwing a checked exception. Or 
you could perhaps put a check for the boolean ExceptionFound in a finally 
clause and throw and exception from there if ExceptionFound == true; such as

} catch (Exception e) {
       System.out.println("Exception found in GenbankSequenceDB --
getSequence");
       System.out.println(e.toString());
       ExceptionFound = true;
       IOExceptionFound = true;
       return null;
     }
//always executed unless system.exit() is called;
finally
{
  // check for state of boolean ExceptionFound here
  if(ExceptionFound)
    {
        //error occured, throw an exception that will be handled further up
        //the stack
        throw new IlllegalAccessionException();
    }
}



just some thoughts.

thanks for your time,

Jess Vermont
Chicago, Il.

Universes of virtually unlimited complexity can be created in the form of 
computer programs. (Joseph Weizenbaum)




>From: James Diggans <jdiggans at excelsiortech.com>
>To: biojava-l at biojava.org
>Subject: [Biojava-l] Errors to STDOUT in BioJava?
>Date: Sat, 20 Nov 2004 23:12:49 -0500
>
>
>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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