[Biojava-l] Depreciated methods

Hamed, Ahmed A. ahmed.elmasri at gmail.com
Mon Jan 26 17:24:20 UTC 2009

Thanks Richard!

For the deprecated methods, is there a reference or a wiki that maps the
deprecated ones to ones that should be used instead?

As for the examples I am having trouble with: WriteToFasta is one. Here is
the error that I am getting:
java.lang.IllegalArgumentException: No alphabet was set in the identifier
    at org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:928)
    at examples.WriteToFasta.main(WriteToFasta.java:43)

And here is my parameter value:
      //get the int constant for the file type
      int fileType = Integer.parseInt("2");

I would appreciate any help.
Best wishes,

On Mon, Jan 26, 2009 at 3:10 AM, Richard Holland
<holland at eaglegenomics.com>wrote:

> > I am new to BioJava and I have been trying some of its examples. I came
> > across some of the depreciated methods and I am not sure if they will be
> > removed entirely any time soon?
> Deprecated = may be removed without notice in any future release. I
> couldn't say for any individual method, but in general it's a bad idea
> to use anything that is marked deprecated when writing new code.
> > I also found some of the examples
> > problematic and didn't run properly even though I am following the
> > instructions stated in the comment section.
> Could you specify exactly which examples didn't work, and the exact
> problems you had with them?
> thanks,
> Richard
> > Please let me know if you have answers for my questions.
> > Best wishes,
> > Ahmed
> >
> --
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> M: +44 7500 438846 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/

Ahmed Abdeen Hamed
Scientific Informatics Project Leader
Marine Biological Laboratory Woods Hole, MA
Ph.D. student, Complex Systems
School of Informatics, Indiana University

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