RE: [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 <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
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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