[Biojava-dev] Proposed change to RichFormat interface

[Michael Heuer]

Mark Schreiber wrote:

> Hi all -
>
> I would like to propose a change  to the RichFormat interface. I think we
> should do this now as we haven't done a stable biojavax roll out yet so
> interface
> changes should still be allowed. The additional methods would be:
>
> public String currentLine();
> public int currentLineNumber();
>
> This would make debugging a lot easier, it would also make construction of
> a RichSeqIOListener that logs and debugs much easier. I was trying to do
> this a while back. I started a background process that parsed 6GB of
> genbank records looking for records that failed. It worked ok but would be
>
> much better with the ability to query the RichFormat in the above way. We
> might even be able to make it  a utility that people could run on suspect
> files and generate standard bug reports to make it easier for us to debug
> the parser code.
>
> What do people think??

Another possibility would be to leave this sort of progress tracking up
to the client, in that they could wrap the InputStream in something like
an CountingInputStream before passing it to the parser(s):

http://jakarta.apache.org/commons/io/api-release/org/apache/commons/io/input/CountingInputStream.html

   michael