[Biojava-dev] exceptions

[Thomas Down]

Once upon a time, Matthew Pocock wrote:
> Ok - nucked NestedException & friends. Checked in all
> my changes. Also, updated demos to work with these API
> changes.

Cool.

> I've fixed a couple of glitches in compiling demos on
> the main trunk. A couple of things aren't easy to fix:
> 
> ssaha\CreateDNAFastaHashTableCompact.java was using
> SeqIOTools to guess sequence format from a File. This
> funcitonality is no longer in SeqIOTools - it is
> needed. I don't care if 10% of the time the guess is
> wrong or blows chunks. I just want it to work 90% of
> the time.

SeqIOTools.guessFileType is still there.  What are you
missing?  Is it something that got changed when Mark
made some improvements to SeqIOTools a few weeks ago.
All I did was remove SeqAlignReadWrite.java, which duplicated
some of the SeqIOTools methods.

> Also, in build.xml, the junit tasks seem to have
> dissapeared. Was that an accident that happened while
> merging the 1.4 trees in?

Really?  it's still working for me.

Did you have a modified build.xml file which got messed
up when CVS merged it with the new revision?

    Thomas.